Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A0 F0 I1 R1
|
155 |
25.8 |
2285122 |
88.0% |
2010907 |
104.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
3,529,526 |
+G |
intergenic (‑40/‑264) |
secA ← / → h16_A3265 |
preprotein translocase subunit SecA/Hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 3,529,524 | 1 | . | G | 100.0%
| 60.7
/ NA
| 17 | intergenic (‑38/‑266) | secA/h16_A3265 | preprotein translocase subunit SecA/Hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (8/9); total (8/9) |
CGTGCGGCGATATTGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCA‑GGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGG‑CGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGC > AM260479/3529415‑3529641
|
cGTGCGGCGATATTGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGcc < 1:1139142/134‑1 (MQ=255)
tGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCcgg < 1:220024/116‑1 (MQ=255)
tGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCcgg > 2:220024/1‑116 (MQ=255)
aTCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCA‑g < 1:290234/92‑1 (MQ=255)
aTCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCA‑g > 2:290234/1‑92 (MQ=255)
cAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTg > 2:29263/1‑134 (MQ=255)
tCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGcc < 2:710470/106‑1 (MQ=255)
tCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGcc > 1:710470/1‑106 (MQ=255)
aTTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCaaa < 1:29263/132‑1 (MQ=255)
gCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCaaaa < 1:1125517/103‑1 (MQ=255)
gCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCaaaa > 2:1125517/1‑103 (MQ=255)
gCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCAcgg‑c < 1:242266/134‑1 (MQ=255)
gTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCAcgg‑ccgg > 2:532624/1‑130 (MQ=255)
catcGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCg < 1:571712/70‑1 (MQ=255)
catcGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCg > 2:571712/1‑70 (MQ=255)
cgGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAggg < 1:532624/134‑1 (MQ=255)
gggCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGggcaggc > 1:1115868/1‑132 (MQ=255)
gcACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCg > 1:333396/1‑37 (MQ=37)
gcACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCg < 2:333396/37‑1 (MQ=37)
|
CGTGCGGCGATATTGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCA‑GGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGG‑CGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGC > AM260479/3529415‑3529641
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TCCAGCGCATTGATCTGCGCCACCGTGCGGCGATATTGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCA‑GGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGG‑CGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTC > AM260479/3529392‑3529673
|
gggctcggagatgtgtataagagacaGCGGCGATATTGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTC < GWNJ‑0478:712:GW2002102894th:2:1201:7411:50719/123‑1 (MQ=60)
acagACCGTGCGGCGATATTGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAA < GWNJ‑0478:712:GW2002102894th:2:1112:7026:75089/146‑1 (MQ=60)
CCGTGCGGCGATATTGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGAT < GWNJ‑0478:712:GW2002102894th:2:2216:1659:83248/150‑1 (MQ=60)
cctttagtggattgtttttttttttttttttttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagccccagGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATT < GWNJ‑0478:712:GW2002102894th:2:2114:15631:5886/43‑1 (MQ=60)
acgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATT < GWNJ‑0478:712:GW2002102894th:2:1216:19713:87198/100‑1 (MQ=60)
TGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATctgtctcttatac > GWNJ‑0478:712:GW2002102894th:2:2109:16281:44651/1‑136 (MQ=60)
atgtgtataagagacagGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCAT < GWNJ‑0478:712:GW2002102894th:2:2216:5370:17422/133‑1 (MQ=60)
tttttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacaGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCAT < GWNJ‑0478:712:GW2002102894th:2:2115:4649:42236/77‑1 (MQ=60)
CATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCA < GWNJ‑0478:712:GW2002102894th:2:1103:1990:88318/148‑1 (MQ=60)
GGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGC < GWNJ‑0478:712:GW2002102894th:2:1115:3030:87062/150‑1 (MQ=60)
cgtgggctcggagatgtgtataagagacagccccagGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGG < GWNJ‑0478:712:GW2002102894th:2:1214:14512:44123/113‑1 (MQ=60)
GCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaataaaccatggagagaac > GWNJ‑0478:712:GW2002102894th:2:1110:17015:39266/1‑57 (MQ=60)
CACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCA > GWNJ‑0478:712:GW2002102894th:2:2215:16369:71445/1‑148 (MQ=60)
GCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCtgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaaaaacaaaacaagtgcaacggatcccatggacg > GWNJ‑0478:712:GW2002102894th:2:1115:17881:101149/1‑43 (MQ=60)
GCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATtgattctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaata > GWNJ‑0478:712:GW2002102894th:2:1205:12067:23531/1‑62 (MQ=60)
GCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCC < GWNJ‑0478:712:GW2002102894th:2:1215:6438:91935/150‑1 (MQ=60)
GAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCActgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgctt > GWNJ‑0478:712:GW2002102894th:2:1212:5633:34457/1‑85 (MQ=60)
GCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaagagaagaaaaaagaaaatactt > GWNJ‑0478:712:GW2002102894th:2:1210:2534:55548/1‑52 (MQ=60)
GCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaaaacgacgaaaactcaat > GWNJ‑0478:712:GW2002102894th:2:1114:19880:61874/1‑52 (MQ=60)
GCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCtgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaa > GWNJ‑0478:712:GW2002102894th:2:1102:18938:14063/1‑81 (MQ=60)
CCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCctgcctcttatacacatctccgagcccacgagacactcgctaaactcgtatgccgtcttctgcttgaaaaaaaaaaaa > GWNJ‑0478:712:GW2002102894th:2:1214:10026:2541/1‑71 (MQ=60)
CCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGT > GWNJ‑0478:712:GW2002102894th:2:1113:3463:82607/1‑150 (MQ=60)
GGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTC > GWNJ‑0478:712:GW2002102894th:2:2101:7577:9524/1‑150 (MQ=60)
|
TCCAGCGCATTGATCTGCGCCACCGTGCGGCGATATTGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCA‑GGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGG‑CGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGTGTGGTC > AM260479/3529392‑3529673
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
