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
|
149 |
26.7 |
2337422 |
87.5% |
2045244 |
105.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260480 |
1,326,746 |
+G |
intergenic (+47/‑123) |
h16_B1172 → / → h16_B1173 |
Amidase/MFS transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260480 | 1,326,745 | 1 | . | G | 96.3%
| 99.1
/ ‑3.0
| 27 | intergenic (+46/‑124) | h16_B1172/h16_B1173 | Amidase/MFS transporter |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base G (14/12); total (15/12) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CGTGCTGATACGGCTGGCCTATGCGGCCGAGCAGGCCTTGCGCGCGCGCCGGCCGCCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑C‑GACAC‑GCGGCGACAA‑GTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACAAAGATGGGCGCAGAAACAGTAGTTCAATCGCCGAATTCCCCACAGCAGCATGAGCTCGACCGG > AM260480/1326618‑1326865
|
cGTGCTGATACGGCTGGCCTATGCGGCCGAGCAGGCCTTGCGCGCGCGCCGGCCGCCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCccgc‑c‑ggacac > 2:824455/1‑129 (MQ=255)
gATACGGCTGGCCTATGCGGCCGAGCAGGCCTTGCGCGCGCGCCGGCCGCCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACAc‑ggcggc > 1:412051/1‑129 (MQ=255)
gATACGGCTGGCCTATGCGGCCGAGCAGGCCTTGCGCGCGCGCCGGCCGCCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACAc‑ggcggc > 2:1100763/1‑129 (MQ=255)
aTACGGCTGGCCTATGCGGCCGAGCAGGCCTTGCGCGCGCGCCGGCCGCCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACAc‑ggcggc < 1:1100763/133‑6 (MQ=255)
gCAGGCCTTGCGCGCGCGCCGGCCGCCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGa > 1:473848/1‑134 (MQ=255)
ccTTGCGCGCGCGCCGGCCGCCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGCTG‑GACACGGCGGCGACAAGGTCGCGAACATAGCGCGACAAcc > 1:828772/1‑134 (MQ=255)
ccggccgCCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACgaggag > 2:765815/1‑134 (MQ=255)
ccggccgCCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACgaggag > 2:695710/1‑134 (MQ=255)
ccggccgCCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACgaggag > 2:518028/1‑134 (MQ=255)
ggccgCCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACg > 1:584813/1‑127 (MQ=255)
ggccgCCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACg < 2:584813/127‑1 (MQ=255)
ccgcATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACa > 1:425455/1‑133 (MQ=255)
cgcATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACaaa < 1:765815/134‑1 (MQ=255)
tgcggCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAA‑g < 1:297847/80‑1 (MQ=255)
tgcggCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAA‑g > 2:297847/5‑84 (MQ=255)
gcTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACAAAGATGGGCGCAGaaa > 1:120217/1‑132 (MQ=255)
aaTAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACAAAGATGGGCGCAGAAACagtagt < 2:412051/134‑1 (MQ=255)
gcgcgcgcCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACAAAGATGGGCGCAGAAACAGTAGTTCAAt < 1:824455/134‑1 (MQ=255)
cgcgcCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACAAAGATGGGCGCAGAAACAGTAGTTCAATCGc < 1:343278/134‑1 (MQ=255)
cGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAAc < 2:668844/86‑1 (MQ=255)
cGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCCAAAc > 1:668844/1‑86 (MQ=255)
ctctACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACAAAGATGGGCGCAGAAACAGTAGTTCAATCGCCGAATTCCCCACAGCAGCATGAGCt < 1:592731/133‑1 (MQ=255)
tACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACAAAGATGGGCGCAGAAACAGTAGTTCAATCGCCGAATTCCCCACAGCAGCATGAGCTCGAc > 2:508146/1‑134 (MQ=255)
tACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACAAAGATGGGCGCAGAAACAGTAGTTCAATCGCCGAATTCCCCACAGCAGCATGAGCTCGAc > 2:869742/1‑134 (MQ=255)
aCAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACAAAGATGGGCGCAGAAACAGTAGTTCAATCGCCGAATTCCCCACAGCAGCATGAGCTCGAcc > 2:425005/1‑134 (MQ=255)
cAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACAAAGATGGGCGCAGAAACAGTAGTTCAATCGCCGAATTCCCCACAGCAGCATGAGCTCGAc < 1:695710/132‑1 (MQ=255)
cAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACAAAGATGGGCGCAGAAACAGTAGTTCAATCGCCGAATTCCCCACAGCAGCATGAGCTCGACCg < 2:544283/134‑1 (MQ=255)
aaaCGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACAAAGATGGGCGCAGAAACAGTAGTTCAATCGCCGAATTCCCCACAGCAGCATGAGCTCGACCgg < 2:425455/134‑1 (MQ=255)
|
CGTGCTGATACGGCTGGCCTATGCGGCCGAGCAGGCCTTGCGCGCGCGCCGGCCGCCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑C‑GACAC‑GCGGCGACAA‑GTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACAAAGATGGGCGCAGAAACAGTAGTTCAATCGCCGAATTCCCCACAGCAGCATGAGCTCGACCGG > AM260480/1326618‑1326865
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ 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
GCCTTTCACCGAACCCGTGCTGATACGGCTGGCCTATGCGGCCGAGCAGGCCTTGCGCGCGCGCCGGCCGCCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑C‑GACAC‑GCGGCGACAA‑GTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACAAAGATGGGCGCAGAAACAGTAGTTCAATCGCCGAATTCCCCACAGCAGCATGAGCTCGACCGGGCCATGGATGGCATCGGGGTG > AM260480/1326603‑1326886
|
GCCTTTCACCGAACCCGTGCTGATACGGCTGGCCTATGCGGCCGAGCAGGCCTTGCGCGCGCGCCGGCCGCCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACAC < GWNJ‑0478:712:GW2002102894th:2:2216:5760:33173/149‑1 (MQ=60)
GCCTTTCACCGAACCCGTGCTGATACGGCTGGCCTATGCGGCCGAGCAGGCCTTGCGCGCGCGCCGGCCGCCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑C‑Ggacacc > GWNJ‑0478:712:GW2002102894th:2:1101:9888:9503/1‑144 (MQ=60)
CACCGAACCCGTGCTGATACGGCTGGCCTATGCGGCCGAGCAGGCCTTGCGCGCGCGCCGGCCGCCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCG > GWNJ‑0478:712:GW2002102894th:2:1208:10050:85564/1‑150 (MQ=60)
GATACGGCTGGCCTATGCGGCCGAGCAGGCCTTGCGCGCGCGCCGGCCGCCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGAC < GWNJ‑0478:712:GW2002102894th:2:2213:15570:97780/149‑1 (MQ=60)
gtgtctcgtgggctcggagatgtgtataagagacaggatacggctggcctatgcgGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCG < GWNJ‑0478:712:GW2002102894th:2:1201:11950:87345/95‑1 (MQ=60)
GGCCTATGCGGCCGAGCAGGCCTTGCGCGCGCGCCGGCCGCCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGAC > GWNJ‑0478:712:GW2002102894th:2:1213:8027:18229/1‑150 (MQ=60)
ATGCGGCCGAGCAGGCCTTGCGCGCGCGCCGGCCGCCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGCTG‑GACACGGCGGCGACAAGGTCGCGAACATAGCGCGACAACCT > GWNJ‑0478:712:GW2002102894th:2:2114:3405:9221/1‑150 (MQ=60)
CCTTGCGCGCGCGCCGGCCGCCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGG > GWNJ‑0478:712:GW2002102894th:2:2101:3994:66079/1‑148 (MQ=60)
ttccaGCGCCGGCCGCCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACAA > GWNJ‑0478:712:GW2002102894th:2:1209:10154:61706/6‑149 (MQ=60)
CCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACAAAGATGGGCGCAGAAAC < GWNJ‑0478:712:GW2002102894th:2:2113:13315:4932/150‑1 (MQ=60)
GCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACAAAGATGGGCGCAGAAAC > GWNJ‑0478:712:GW2002102894th:2:1108:6118:44350/1‑148 (MQ=60)
GGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCCAAACGAGGAGGAGACAAAGctgtctcttatacacatctccgagcccacgagac > GWNJ‑0478:712:GW2002102894th:2:2107:19483:75775/1‑116 (MQ=60)
GGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACAAAGATGGGCGCAGAAACAGTAGTTCAATCGCCGAATTCCCCAC < GWNJ‑0478:712:GW2002102894th:2:2115:19165:88838/150‑1 (MQ=60)
GCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACAAAGATGGGCGCAGAAACAGTAGTTCAATCGCCGAATTCCCCACAGC < GWNJ‑0478:712:GW2002102894th:2:1205:5758:77774/150‑1 (MQ=60)
GCTCTACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACAAAGATGGGCGCAGAAACAGTAGTTCAATCGCCGAATTCCCCACAGCAGCATGAGCTCGACCGGGCCATGGA < GWNJ‑0478:712:GW2002102894th:2:2103:9486:17041/149‑1 (MQ=60)
ACAAACGCCCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACAAAGATGGGCGCAGAAACAGTAGTTCAATCGCCGAATTCCCCACAGCAGCATGAGCTCGACCGGGCCATGGATGGC < GWNJ‑0478:712:GW2002102894th:2:2108:19320:34210/148‑1 (MQ=60)
CCGC‑CGGACACGGCGGCGACAAGGTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACAAAGATGGGCGCAGAAACAGTAGTTCAATCGCCGAATTCCCCACAGCAGCATGAGCTCGACCGGGCCATGGActgtctcttatac > GWNJ‑0478:712:GW2002102894th:2:2202:16766:6545/1‑136 (MQ=60)
|
GCCTTTCACCGAACCCGTGCTGATACGGCTGGCCTATGCGGCCGAGCAGGCCTTGCGCGCGCGCCGGCCGCCGCATTCGACGCCGGCGCTGGAATAGGCGCGCGCCGGAACGACGTTTTATCGCTGCTCTACAAACGCCCGC‑C‑GACAC‑GCGGCGACAA‑GTCGCGGACATAGCGCGACAACCTCGAAACGAGGAGGAGACAAAGATGGGCGCAGAAACAGTAGTTCAATCGCCGAATTCCCCACAGCAGCATGAGCTCGACCGGGCCATGGATGGCATCGGGGTG > AM260480/1326603‑1326886
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
