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
|
146 |
27.9 |
2327082 |
89.7% |
2087392 |
107.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
547,879 |
2 bp→GA |
coding (595‑596/630 nt) |
h16_A0522 ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 547,879 | 0 | A | G | 100.0%
| 90.7
/ NA
| 24 | L199S (CTC→TCC) | h16_A0522 | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (14/10); total (14/10) |
| * | AM260479 | 547,880 | 0 | G | A | 100.0%
| 89.9
/ NA
| 24 | L199S (CTC→TCC) | h16_A0522 | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (14/10); total (14/10) |
CATGGGTTGCGACATGAATCGTAT‑CAACAGGTTGTAGCGCGCGCCCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGAGCAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTGCCGCCGCGGCTGCCTGCAGCCGGGAAGCGTGCGTC > AM260479/547794‑548003
||
cATGGGTTGCGACATGAATCGTATCCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAgg > 2:153736/1‑134 (MQ=255)
aaCAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCa < 2:71830/96‑1 (MQ=255)
aaCAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCa > 1:71830/1‑96 (MQ=255)
aaCAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCcgcg < 2:279600/128‑1 (MQ=255)
aaCAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCcgcg > 1:279600/1‑128 (MQ=255)
aCAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGcc > 1:32098/1‑86 (MQ=255)
aCAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGcc < 2:32098/86‑1 (MQ=255)
tAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCg > 1:374529/1‑134 (MQ=255)
gcgcgcg‑cCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTg < 2:440745/71‑1 (MQ=255)
gcgcgcg‑cCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTg > 1:440745/1‑71 (MQ=255)
gcgcgcg‑cCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTg > 1:379521/1‑71 (MQ=255)
gcgcgcg‑cCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTg < 2:379521/71‑1 (MQ=255)
cgcgccGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGt > 1:27712/5‑130 (MQ=255)
cgcgccGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGt < 2:27712/126‑1 (MQ=255)
ccGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCcgc < 2:377105/121‑1 (MQ=255)
ccGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCcgc > 1:377105/1‑121 (MQ=255)
gCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTgccgcc > 1:868616/1‑134 (MQ=255)
agcagcGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTGCCGCCGCGGctg < 1:153736/134‑1 (MQ=255)
gcggcgAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTc < 2:1037623/47‑1 (MQ=38)
gcggcgAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTc > 1:1037623/1‑47 (MQ=38)
gcggcgAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTGCCGCCGCGGctgcctg > 1:297843/1‑132 (MQ=255)
gcgAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTGCCGCCGCGGCTGCCTGCAGcc > 1:913116/1‑134 (MQ=255)
aGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTGCCGCCGCGGCTGCCTGCAGCCggg > 1:921876/1‑132 (MQ=255)
ccACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTGCCGCCGCGGCTGCCTGCAGCCGGGAAGCGTGCGTc < 2:921876/133‑1 (MQ=255)
||
CATGGGTTGCGACATGAATCGTAT‑CAACAGGTTGTAGCGCGCGCCCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGAGCAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTGCCGCCGCGGCTGCCTGCAGCCGGGAAGCGTGCGTC > AM260479/547794‑548003
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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
CTTGGGTGGCAGCTCTTCGGTGAACAGTTCGATCAGCAGCGAGTCGGTCATGGGTTGCGACATGAATCGTAT‑CAACAGGTTGTAGCGCGCGCCCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGAGCAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTGCCGCCGCGGCTGCCTGCAGCCGGGAAGCGTGCGTCGATGCGGCGCAGGC > AM260479/547746‑548017
|
ttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacaggtatcCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGC < GWNJ‑0478:712:GW2002102894th:2:1214:6942:9773/76‑1 (MQ=60)
gcgcggcgaaagattaggttccactccggacagcagccacaggcCCGCTTGTCAGCAGGCCGGCCGGGGCCGGAAAAAAGGAATTTTAAGGGGTTTTCCCCAACCTTCCCCGGGGAACCAAGGCCAAGGCCCCAACCAAGGGGCCCCGTTCTGTTGCCGGAATTGCAGC < GWNJ‑0478:712:GW2002102894th:2:2210:14975:40496/1‑4294967218 (MQ=60)
GTTGCGACATGAATCGTATCCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCtgtctcttatacacatctcc > GWNJ‑0478:712:GW2002102894th:2:1110:2532:90151/1‑130 (MQ=60)
GTTGCGACATGAATCGTATCCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACCCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCtgtctcttatacacatctcc > GWNJ‑0478:712:GW2002102894th:2:1115:9850:47069/1‑130 (MQ=60)
ACATGAATCGTATCCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCctgtctcttatacacatctccg > GWNJ‑0478:712:GW2002102894th:2:1104:13408:46938/1‑126 (MQ=60)
ACATGAATCGTATCCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGG > GWNJ‑0478:712:GW2002102894th:2:1116:12593:58640/1‑150 (MQ=60)
CATGAATCGTATCCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGctgtctcttatacacatctccgagcccacgagac > GWNJ‑0478:712:GW2002102894th:2:1105:15458:4084/1‑116 (MQ=60)
GTATCCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGT > GWNJ‑0478:712:GW2002102894th:2:1207:9283:35604/1‑150 (MQ=60)
atcCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCtgtctcttatacacatctccgagcccacgagacactcgctaatctcgt > GWNJ‑0478:712:GW2002102894th:2:1207:15818:63057/4‑102 (MQ=60)
atcCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCtgtctcttatacacatctccgagcccacgagacactcgctaatctcgt > GWNJ‑0478:712:GW2002102894th:2:1211:11420:3526/4‑102 (MQ=60)
CAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTG > GWNJ‑0478:712:GW2002102894th:2:1103:4344:76352/1‑150 (MQ=60)
cgagcttagcgagtgtctcgtgggctcggagatgtgtataagagacagGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTG < GWNJ‑0478:712:GW2002102894th:2:2208:16007:74625/102‑1 (MQ=60)
AGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCaatgcgcctac > GWNJ‑0478:712:GW2002102894th:2:1207:14439:49790/1‑138 (MQ=60)
GTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTGCCGCCG > GWNJ‑0478:712:GW2002102894th:2:2116:9305:93732/1‑150 (MQ=60)
gagacaGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCaatgcgcctacaccacgctgcaa < GWNJ‑0478:712:GW2002102894th:2:1204:20313:79177/144‑24 (MQ=60)
CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaa > GWNJ‑0478:712:GW2002102894th:2:2211:2544:81481/1‑77 (MQ=60)
CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTGCCGCCGCGGCTGCCTGC > GWNJ‑0478:712:GW2002102894th:2:1201:13673:70993/1‑148 (MQ=60)
CTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTGCCGCCGCGGCTGCCTGCAGCCG > GWNJ‑0478:712:GW2002102894th:2:2202:1613:73092/1‑150 (MQ=60)
CAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTGCCGCCGCGGCTGCCTGCAGCCGGGAAG < GWNJ‑0478:712:GW2002102894th:2:1111:9439:13932/150‑1 (MQ=60)
CAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTGCCGCCGCGGCTGCCTGCAGCCGGGA > GWNJ‑0478:712:GW2002102894th:2:2204:12769:26493/1‑148 (MQ=60)
GTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTGCCGCCGCGGCTGCCTGCAGCCGGGAAGCtgtctcttatacacatctccg > GWNJ‑0478:712:GW2002102894th:2:1215:9156:48236/1‑129 (MQ=60)
|
CTTGGGTGGCAGCTCTTCGGTGAACAGTTCGATCAGCAGCGAGTCGGTCATGGGTTGCGACATGAATCGTAT‑CAACAGGTTGTAGCGCGCGCCCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGAGCAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTGCCGCCGCGGCTGCCTGCAGCCGGGAAGCGTGCGTCGATGCGGCGCAGGC > AM260479/547746‑548017
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
