funcotator/forum_info/forum_post_human_reference_discrepancies.md

<a name="0"></a>
## 0 - Introduction
This page explains the discrepancies between the different "hg19" references.

There are 4 common "hg19" references, and they are NOT directly interchangeable:
* **hg19** (`ucsc.hg19.fasta`, MD5sum: `a244d8a32473650b25c6e8e1654387d6`)
* **b37** (`Homo_sapiens_assembly19.fasta`, MD5sum: `886ba1559393f75872c1cf459eb57f2d`)
* **GRCh37** (`GRCh37.p13.genome.fasta`, MD5sum: `c140882eb2ea89bc2edfe934d51b66cc`)
* **humanG1Kv37** (`human_g1k_v37.fasta`, MD5sum: `0ce84c872fc0072a885926823dcd0338`)

<a name="0.1"></a>
### 0.1 - Table of Contents
0. [0.0 Introduction](#0)
    1. [0.1 Table of Contents](#0.1)
1. [hg19](#hg19)
2. [GRCh37](#grch37)
3. [b37](#b37)
4. [HumanG1Kv37](#humanG1Kv37)
5. [Reference Comparison Table](#comparison)
6. [Additional Information](#additional)

<a name="grch37"></a>
## GRCh37
The Genome Reference Consortium Human Build 37, *GRCh37*, (`GRCh37.p13.genome.fasta`, MD5sum: `c140882eb2ea89bc2edfe934d51b66cc`) is a _Homo Sapiens_ genome reference file built by the Genome Reference Consortium.  This is a baseline human genome reference and serves as the basis for the other three references in this comparison.

For more information on GRCh37, visit the [official Genome Reference Consortium website](https://www.ncbi.nlm.nih.gov/grc).

<a name="hg19"></a>
## hg19
The University of California at Santa Cruz (UCSC) has created a reference based on [GRCh37](#grch37).  This reference is often referred to as *hg19* (`ucsc.hg19.fasta`, MD5sum: `a244d8a32473650b25c6e8e1654387d6`).

This reference contains some alterations from the baseline reference from the Genome Reference Consortium.  These alterations largely consist of contig name changes, however there are *known sequence differences on some contigs as well*.

For details see the [comparison table](#comparison).

<a name="b37"></a>
## b37
The Broad Institute created a human genome reference file based on [GRCh37](#grch37).  This reference is often referred to as *b37* (`Homo_sapiens_assembly19.fasta`, MD5sum: `886ba1559393f75872c1cf459eb57f2d`).

**When people at The Broad Institute's Genomics Platform refer to the _hg19_ reference, they are actually referring to `b37`.**

This reference contains some alterations from the baseline reference from the Genome Reference Consortium.  These alterations largely consist of contig name changes, however there are *known sequence differences on some contigs as well*.

Anecdotally the changes are for bases for which there was low confidence.  Those low confidence bases were then masked out in the `b37` reference to be the `IUPAC` symbol for any base.  However, _there does not seem to be a detailed comparison readily available_.

For details see the [comparison table](#comparison).

<a name="humanG1Kv37"></a>
## HumanG1Kv37
The *humanG1Kv37* (`human_g1k_v37.fasta`, MD5sum: `0ce84c872fc0072a885926823dcd0338`)  reference is equivalent to [b37](#b37), with the exception that it does not contain the decoy sequence for human herpesvirus 4 type 1 (named _NC_007605_).

<a name="comparison"></a>
## Reference Comparison Table

The specific differences between these four references are detailed in the following table.

The contigs with identical MD5sums are specified in each row.  In the case that the MD5sum does not match between the references (indicating a sequence difference), the row will have a blank entry for that contig (`----`).

Primary contigs with differing MD5sums are highlighted in red.
Alternate contigs with differing MD5sums are highlighted in orange.

<table>
<tr><th>MD5</th><th>HumanG1Kv37 Contig</th><th>B37 Contig</th><th>HG19 Contig</th><th>GRCh37 Contig</th></tr>
<tr><td>06cbf126247d89664a4faebad130fe9c</td><td>GL000202.1</td><td>GL000202.1</td><td>chr11_gl000202_random</td><td>GL000202.1</td></tr>
<tr><td>0996b4475f353ca98bacb756ac479140</td><td>GL000244.1</td><td>GL000244.1</td><td>chrUn_gl000244</td><td>GL000244.1</td></tr>
<tr><td>118a25ca210cfbcdfb6c2ebb249f9680</td><td>GL000235.1</td><td>GL000235.1</td><td>chrUn_gl000235</td><td>GL000235.1</td></tr>
<tr><td>131b1efc3270cc838686b54e7c34b17b</td><td>GL000238.1</td><td>GL000238.1</td><td>chrUn_gl000238</td><td>GL000238.1</td></tr>
<tr><td>1c1b2cd1fccbc0a99b6a447fa24d1504</td><td>GL000226.1</td><td>GL000226.1</td><td>chrUn_gl000226</td><td>GL000226.1</td></tr>
<tr><td>1d708b54644c26c7e01c2dad5426d38c</td><td>GL000218.1</td><td>GL000218.1</td><td>chrUn_gl000218</td><td>GL000218.1</td></tr>
<tr><td>1d78abec37c15fe29a275eb08d5af236</td><td>GL000249.1</td><td>GL000249.1</td><td>chrUn_gl000249</td><td>GL000249.1</td></tr>
<tr><td>2f8694fc47576bc81b5fe9e7de0ba49e</td><td>GL000242.1</td><td>GL000242.1</td><td>chrUn_gl000242</td><td>GL000242.1</td></tr>
<tr><td>3238fb74ea87ae857f9c7508d315babb</td><td>GL000221.1</td><td>GL000221.1</td><td>chrUn_gl000221</td><td>GL000221.1</td></tr>
<tr><td>325ba9e808f669dfeee210fdd7b470ac</td><td>GL000192.1</td><td>GL000192.1</td><td>chr1_gl000192_random</td><td>GL000192.1</td></tr>
<tr><td>399dfa03bf32022ab52a846f7ca35b30</td><td>GL000223.1</td><td>GL000223.1</td><td>chrUn_gl000223</td><td>GL000223.1</td></tr>
<tr><td>3e06b6741061ad93a8587531307057d8</td><td>GL000232.1</td><td>GL000232.1</td><td>chrUn_gl000232</td><td>GL000232.1</td></tr>
<tr><td>43f69e423533e948bfae5ce1d45bd3f1</td><td>GL000206.1</td><td>GL000206.1</td><td>chr17_gl000206_random</td><td>GL000206.1</td></tr>
<tr><td>445a86173da9f237d7bcf41c6cb8cc62</td><td>GL000240.1</td><td>GL000240.1</td><td>chrUn_gl000240</td><td>GL000240.1</td></tr>
<tr><td>46c2032c37f2ed899eb41c0473319a69</td><td>GL000214.1</td><td>GL000214.1</td><td>chrUn_gl000214</td><td>GL000214.1</td></tr>
<tr><td>563531689f3dbd691331fd6c5730a88b</td><td>GL000212.1</td><td>GL000212.1</td><td>chrUn_gl000212</td><td>GL000212.1</td></tr>
<tr><td>569af3b73522fab4b40995ae4944e78e</td><td>GL000199.1</td><td>GL000199.1</td><td>chr9_gl000199_random</td><td>GL000199.1</td></tr>
<tr><td>5a8e43bec9be36c7b49c84d585107776</td><td>GL000248.1</td><td>GL000248.1</td><td>chrUn_gl000248</td><td>GL000248.1</td></tr>
<tr><td>5d9ec007868d517e73543b005ba48535</td><td>GL000195.1</td><td>GL000195.1</td><td>chr7_gl000195_random</td><td>GL000195.1</td></tr>
<tr><td>5eb3b418480ae67a997957c909375a73</td><td>GL000215.1</td><td>GL000215.1</td><td>chrUn_gl000215</td><td>GL000215.1</td></tr>
<tr><td>63945c3e6962f28ffd469719a747e73c</td><td>GL000225.1</td><td>GL000225.1</td><td>chrUn_gl000225</td><td>GL000225.1</td></tr>
<tr><td>642a232d91c486ac339263820aef7fe0</td><td>GL000216.1</td><td>GL000216.1</td><td>chrUn_gl000216</td><td>GL000216.1</td></tr>
<tr><td>6ac8f815bf8e845bb3031b73f812c012</td><td>GL000194.1</td><td>GL000194.1</td><td>chr4_gl000194_random</td><td>GL000194.1</td></tr>
<tr><td>6d243e18dea1945fb7f2517615b8f52e</td><td>GL000217.1</td><td>GL000217.1</td><td>chrUn_gl000217</td><td>GL000217.1</td></tr>
<tr><td>6f5efdd36643a9b8c8ccad6f2f1edc7b</td><td>GL000197.1</td><td>GL000197.1</td><td>chr8_gl000197_random</td><td>GL000197.1</td></tr>
<tr><td>6fe9abac455169f50470f5a6b01d0f59</td><td>GL000222.1</td><td>GL000222.1</td><td>chrUn_gl000222</td><td>GL000222.1</td></tr>
<tr><td>75e4c8d17cd4addf3917d1703cacaf25</td><td>GL000200.1</td><td>GL000200.1</td><td>chr9_gl000200_random</td><td>GL000200.1</td></tr>
<tr><td>7daaa45c66b288847b9b32b964e623d3</td><td>GL000211.1</td><td>GL000211.1</td><td>chrUn_gl000211</td><td>GL000211.1</td></tr>
<tr><td>7de00226bb7df1c57276ca6baabafd15</td><td>GL000247.1</td><td>GL000247.1</td><td>chrUn_gl000247</td><td>GL000247.1</td></tr>
<tr><td>7e0e2e580297b7764e31dbc80c2540dd</td><td>X</td><td>X</td><td>chrX</td><td>chrX</td></tr>
<tr><td>7fed60298a8d62ff808b74b6ce820001</td><td>GL000233.1</td><td>GL000233.1</td><td>chrUn_gl000233</td><td>GL000233.1</td></tr>
<tr><td>851106a74238044126131ce2a8e5847c</td><td>GL000210.1</td><td>GL000210.1</td><td>chr21_gl000210_random</td><td>GL000210.1</td></tr>
<tr><td>868e7784040da90d900d2d1b667a1383</td><td>GL000198.1</td><td>GL000198.1</td><td>chr9_gl000198_random</td><td>GL000198.1</td></tr>
<tr><td>89bc61960f37d94abf0df2d481ada0ec</td><td>GL000245.1</td><td>GL000245.1</td><td>chrUn_gl000245</td><td>GL000245.1</td></tr>
<tr><td>93f998536b61a56fd0ff47322a911d4b</td><td>GL000234.1</td><td>GL000234.1</td><td>chrUn_gl000234</td><td>GL000234.1</td></tr>
<tr><td>96358c325fe0e70bee73436e8bb14dbd</td><td>GL000203.1</td><td>GL000203.1</td><td>chr17_gl000203_random</td><td>GL000203.1</td></tr>
<tr><td>99795f15702caec4fa1c4e15f8a29c07</td><td>GL000239.1</td><td>GL000239.1</td><td>chrUn_gl000239</td><td>GL000239.1</td></tr>
<tr><td>9d424fdcc98866650b58f004080a992a</td><td>GL000213.1</td><td>GL000213.1</td><td>chrUn_gl000213</td><td>GL000213.1</td></tr>
<tr><td>a4aead23f8053f2655e468bcc6ecdceb</td><td>GL000227.1</td><td>GL000227.1</td><td>chrUn_gl000227</td><td>GL000227.1</td></tr>
<tr><td>aa81be49bf3fe63a79bdc6a6f279abf6</td><td>GL000208.1</td><td>GL000208.1</td><td>chr19_gl000208_random</td><td>GL000208.1</td></tr>
<tr><td>b4eb71ee878d3706246b7c1dbef69299</td><td>GL000230.1</td><td>GL000230.1</td><td>chrUn_gl000230</td><td>GL000230.1</td></tr>
<tr><td>ba8882ce3a1efa2080e5d29b956568a4</td><td>GL000231.1</td><td>GL000231.1</td><td>chrUn_gl000231</td><td>GL000231.1</td></tr>
<tr><td>c5a17c97e2c1a0b6a9cc5a6b064b714f</td><td>GL000228.1</td><td>GL000228.1</td><td>chrUn_gl000228</td><td>GL000228.1</td></tr>
<tr><td>cc34279a7e353136741c9fce79bc4396</td><td>GL000243.1</td><td>GL000243.1</td><td>chrUn_gl000243</td><td>GL000243.1</td></tr>
<tr><td>d0f40ec87de311d8e715b52e4c7062e1</td><td>GL000229.1</td><td>GL000229.1</td><td>chrUn_gl000229</td><td>GL000229.1</td></tr>
<tr><td>d22441398d99caf673e9afb9a1908ec5</td><td>GL000205.1</td><td>GL000205.1</td><td>chr17_gl000205_random</td><td>GL000205.1</td></tr>
<tr><td>d5b2fc04f6b41b212a4198a07f450e20</td><td>GL000224.1</td><td>GL000224.1</td><td>chrUn_gl000224</td><td>GL000224.1</td></tr>
<tr><td>d75b436f50a8214ee9c2a51d30b2c2cc</td><td>GL000191.1</td><td>GL000191.1</td><td>chr1_gl000191_random</td><td>GL000191.1</td></tr>
<tr><td>d92206d1bb4c3b4019c43c0875c06dc0</td><td>GL000196.1</td><td>GL000196.1</td><td>chr8_gl000196_random</td><td>GL000196.1</td></tr>
<tr><td>dbb6e8ece0b5de29da56601613007c2a</td><td>GL000193.1</td><td>GL000193.1</td><td>chr4_gl000193_random</td><td>GL000193.1</td></tr>
<tr><td>dfb7e7ec60ffdcb85cb359ea28454ee9</td><td>GL000201.1</td><td>GL000201.1</td><td>chr9_gl000201_random</td><td>GL000201.1</td></tr>
<tr><td>e0c82e7751df73f4f6d0ed30cdc853c0</td><td>GL000237.1</td><td>GL000237.1</td><td>chrUn_gl000237</td><td>GL000237.1</td></tr>
<tr><td>e4afcd31912af9d9c2546acf1cb23af2</td><td>GL000246.1</td><td>GL000246.1</td><td>chrUn_gl000246</td><td>GL000246.1</td></tr>
<tr><td>ef4258cdc5a45c206cea8fc3e1d858cf</td><td>GL000241.1</td><td>GL000241.1</td><td>chrUn_gl000241</td><td>GL000241.1</td></tr>
<tr><td>efc49c871536fa8d79cb0a06fa739722</td><td>GL000204.1</td><td>GL000204.1</td><td>chr17_gl000204_random</td><td>GL000204.1</td></tr>
<tr><td>f3814841f1939d3ca19072d9e89f3fd7</td><td>GL000207.1</td><td>GL000207.1</td><td>chr18_gl000207_random</td><td>GL000207.1</td></tr>
<tr><td>f40598e2a5a6b26e84a3775e0d1e2c81</td><td>GL000209.1</td><td>GL000209.1</td><td>chr19_gl000209_random</td><td>GL000209.1</td></tr>
<tr><td>f977edd13bac459cb2ed4a5457dba1b3</td><td>GL000219.1</td><td>GL000219.1</td><td>chrUn_gl000219</td><td>GL000219.1</td></tr>
<tr><td>fc35de963c57bf7648429e6454f1c9db</td><td>GL000220.1</td><td>GL000220.1</td><td>chrUn_gl000220</td><td>GL000220.1</td></tr>
<tr><td>fdcd739913efa1fdc64b6c0cd7016779</td><td>GL000236.1</td><td>GL000236.1</td><td>chrUn_gl000236</td><td>GL000236.1</td></tr>
<tr><td>1b22b98cdeb4a9304cb5d48026a85128</td><td>1</td><td>1</td><td>chr1</td><td>chr1</td></tr>
<tr><td>a0d9851da00400dec1098a9255ac712e</td><td>2</td><td>2</td><td>chr2</td><td>chr2</td></tr>
<tr><td>23dccd106897542ad87d2765d28a19a1</td><td>4</td><td>4</td><td>chr4</td><td>chr4</td></tr>
<tr><td>0740173db9ffd264d728f32784845cd7</td><td>5</td><td>5</td><td>chr5</td><td>chr5</td></tr>
<tr><td>1d3a93a248d92a729ee764823acbbc6b</td><td>6</td><td>6</td><td>chr6</td><td>chr6</td></tr>
<tr><td>618366e953d6aaad97dbe4777c29375e</td><td>7</td><td>7</td><td>chr7</td><td>chr7</td></tr>
<tr><td>96f514a9929e410c6651697bded59aec</td><td>8</td><td>8</td><td>chr8</td><td>chr8</td></tr>
<tr><td>3e273117f15e0a400f01055d9f393768</td><td>9</td><td>9</td><td>chr9</td><td>chr9</td></tr>
<tr><td>988c28e000e84c26d552359af1ea2e1d</td><td>10</td><td>10</td><td>chr10</td><td>chr10</td></tr>
<tr><td>98c59049a2df285c76ffb1c6db8f8b96</td><td>11</td><td>11</td><td>chr11</td><td>chr11</td></tr>
<tr><td>51851ac0e1a115847ad36449b0015864</td><td>12</td><td>12</td><td>chr12</td><td>chr12</td></tr>
<tr><td>283f8d7892baa81b510a015719ca7b0b</td><td>13</td><td>13</td><td>chr13</td><td>chr13</td></tr>
<tr><td>98f3cae32b2a2e9524bc19813927542e</td><td>14</td><td>14</td><td>chr14</td><td>chr14</td></tr>
<tr><td>e5645a794a8238215b2cd77acb95a078</td><td>15</td><td>15</td><td>chr15</td><td>chr15</td></tr>
<tr><td>fc9b1a7b42b97a864f56b348b06095e6</td><td>16</td><td>16</td><td>chr16</td><td>chr16</td></tr>
<tr><td>351f64d4f4f9ddd45b35336ad97aa6de</td><td>17</td><td>17</td><td>chr17</td><td>chr17</td></tr>
<tr><td>b15d4b2d29dde9d3e4f93d1d0f2cbc9c</td><td>18</td><td>18</td><td>chr18</td><td>chr18</td></tr>
<tr><td>1aacd71f30db8e561810913e0b72636d</td><td>19</td><td>19</td><td>chr19</td><td>chr19</td></tr>
<tr><td>0dec9660ec1efaaf33281c0d5ea2560f</td><td>20</td><td>20</td><td>chr20</td><td>chr20</td></tr>
<tr><td>2979a6085bfe28e3ad6f552f361ed74d</td><td>21</td><td>21</td><td>chr21</td><td>chr21</td></tr>
<tr><td>a718acaa6135fdca8357d5bfe94211dd</td><td>22</td><td>22</td><td>chr22</td><td>chr22</td></tr>
<tr bgcolor="#FD1010"><td>1fa3474750af0948bdf97d5a0ee52e51</td><td>Y</td><td>Y</td><td>----</td><td>----</td></tr>
<tr bgcolor="#EB8B31"><td>6743bd63b3ff2b5b8985d8933c53290a</td><td>----</td><td>NC_007605</td><td>----</td><td>----</td></tr>
<tr bgcolor="#FD1010"><td>c68f52674c9fb33aef52dcf399755519</td><td>MT</td><td>MT</td><td>----</td><td>chrM</td></tr>
<tr bgcolor="#FD1010"><td>fdfd811849cc2fadebc929bb925902e5</td><td>3</td><td>3</td><td>----</td><td>----</td></tr>
<tr bgcolor="#EB8B31"><td>094d037050cad692b57ea12c4fef790f</td><td>----</td><td>----</td><td>chr6_qbl_hap6</td><td>GL000255.1</td></tr>
<tr bgcolor="#EB8B31"><td>18c17e1641ef04873b15f40f6c8659a4</td><td>----</td><td>----</td><td>chr6_cox_hap2</td><td>GL000251.1</td></tr>
<tr bgcolor="#FD1010"><td>1e86411d73e6f00a10590f976be01623</td><td>----</td><td>----</td><td>chrY</td><td>chrY</td></tr>
<tr bgcolor="#EB8B31"><td>2a3c677c426a10e137883ae1ffb8da3f</td><td>----</td><td>----</td><td>chr6_dbb_hap3</td><td>GL000252.1</td></tr>
<tr bgcolor="#EB8B31"><td>3b6d666200e72bcc036bf88a4d7e0749</td><td>----</td><td>----</td><td>chr6_ssto_hap7</td><td>GL000256.1</td></tr>
<tr bgcolor="#FD1010"><td>641e4338fa8d52a5b781bd2a2c08d3c3</td><td>----</td><td>----</td><td>chr3</td><td>chr3</td></tr>
<tr bgcolor="#EB8B31"><td>9d51d4152174461cd6715c7ddc588dc8</td><td>----</td><td>----</td><td>chr6_mann_hap4</td><td>GL000253.1</td></tr>
<tr bgcolor="#FD1010"><td>d2ed829b8a1628d16cbeee88e88e39eb</td><td>----</td><td>----</td><td>chrM</td><td>----</td></tr>
<tr bgcolor="#EB8B31"><td>d89517b400226d3b56e753972a7cad67</td><td>----</td><td>----</td><td>chr17_ctg5_hap1</td><td>GL000258.1</td></tr>
<tr bgcolor="#EB8B31"><td>efed415dd8742349cb7aaca054675b9a</td><td>----</td><td>----</td><td>chr6_mcf_hap5</td><td>GL000254.1</td></tr>
<tr bgcolor="#EB8B31"><td>fa24f81b680df26bcfb6d69b784fbe36</td><td>----</td><td>----</td><td>chr4_ctg9_hap1</td><td>GL000257.1</td></tr>
<tr bgcolor="#EB8B31"><td>fe71bc63420d666884f37a3ad79f3317</td><td>----</td><td>----</td><td>chr6_apd_hap1</td><td>GL000250.1</td></tr>
<tr bgcolor="#EB8B31"><td>0386df1d3476e6649f919195cc072fc7</td><td>----</td><td>----</td><td>----</td><td>GL383574.1</td></tr>
<tr bgcolor="#EB8B31"><td>03de7a950b56720768373120bbddf693</td><td>----</td><td>----</td><td>----</td><td>GL383558.1</td></tr>
<tr bgcolor="#EB8B31"><td>03f5fa89e52d0fe155d2e3968bf2eeb7</td><td>----</td><td>----</td><td>----</td><td>GL339450.1</td></tr>
<tr bgcolor="#EB8B31"><td>049056a72b5aee0b3f876ddf554f0208</td><td>----</td><td>----</td><td>----</td><td>JH720447.1</td></tr>
<tr bgcolor="#EB8B31"><td>063358c8e7f81361b959efab7b3f15cc</td><td>----</td><td>----</td><td>----</td><td>GL383565.1</td></tr>
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<tr bgcolor="#EB8B31"><td>9d197695e8a47d4c30c891a53a0fd588</td><td>----</td><td>----</td><td>----</td><td>JH720451.1</td></tr>
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<tr bgcolor="#EB8B31"><td>a009cf3116a844d7b2d467e672931bc5</td><td>----</td><td>----</td><td>----</td><td>GL383564.1</td></tr>
<tr bgcolor="#EB8B31"><td>a0584071d5a8e88fda38d4cca38704cb</td><td>----</td><td>----</td><td>----</td><td>KB663605.1</td></tr>
<tr bgcolor="#EB8B31"><td>a0bce2b33eb96adcb750622527225e7d</td><td>----</td><td>----</td><td>----</td><td>JH720443.2</td></tr>
<tr bgcolor="#EB8B31"><td>a0f25165c6537c9861cc1231f710e99f</td><td>----</td><td>----</td><td>----</td><td>GL383566.1</td></tr>
<tr bgcolor="#EB8B31"><td>a1dab5e9bbedd3539ace29af1f9d6139</td><td>----</td><td>----</td><td>----</td><td>JH806595.1</td></tr>
<tr bgcolor="#EB8B31"><td>a260ca7327d292deefef4f5fc7346dc4</td><td>----</td><td>----</td><td>----</td><td>GL383561.2</td></tr>
<tr bgcolor="#EB8B31"><td>a2ecd2eb53eb1737423d5a637e4374a9</td><td>----</td><td>----</td><td>----</td><td>JH636058.1</td></tr>
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<tr bgcolor="#EB8B31"><td>aa5b0a15acec3c6177db764bd103d8a0</td><td>----</td><td>----</td><td>----</td><td>JH720453.1</td></tr>
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<tr bgcolor="#EB8B31"><td>adb23c033121d433739de02cfa00c9fb</td><td>----</td><td>----</td><td>----</td><td>JH806582.2</td></tr>
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<tr bgcolor="#EB8B31"><td>faae4c952e9c38254538e1853b786276</td><td>----</td><td>----</td><td>----</td><td>GL582976.1</td></tr>
<tr bgcolor="#EB8B31"><td>fc93038463f9660e139435537ef53a5c</td><td>----</td><td>----</td><td>----</td><td>KB663604.1</td></tr>
<tr bgcolor="#EB8B31"><td>fdeb8db11e8544a638179a592c051331</td><td>----</td><td>----</td><td>----</td><td>JH636061.1</td></tr>
<tr bgcolor="#EB8B31"><td>fef0bc815f4826ea408515d8ec74ca80</td><td>----</td><td>----</td><td>----</td><td>JH636057.1</td></tr>
<tr bgcolor="#EB8B31"><td>ff7c4316cb69a8d571bd7ef85c1a10e4</td><td>----</td><td>----</td><td>----</td><td>JH720455.1</td></tr>
</table>

This table indicates that while most contigs contain the same data, there are several with **sequence differences between the references**.  Among those are **Chromosome 3**, **Chromosome Y**, and the **Mitochondrial Contig**.

Anecdotally the changes are for bases for which there was low confidence, with those low confidence bases masked out to be the `IUPAC` symbol for any base.  However, _there does not seem to be a detailed comparison readily available (i.e. there's no proof that this is true)_.

Therefore, when doing comparisons across the four reference versions for each of these contigs, some care should be taken.

<a name="additional"></a>
## Additional Information
Some further details can be found on [this DNAnexus wiki page](https://wiki.dnanexus.com/scientific-notes/human-genome) as of 2019/01/30.

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