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 |
|
A1 F3 I140 R1
|
11 |
50.8 |
3223530 |
93.3% |
3007553 |
83.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,267,454 |
C→T |
R20C (CGC→TGC) |
soxR → |
redox‑sensitive transcriptional activator SoxR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,267,454 | 0 | C | T | 97.6%
| 158.9
/ ‑5.0
| 42 | R20C (CGC→TGC) | soxR | redox‑sensitive transcriptional activator SoxR |
| Reads supporting (aligned to +/- strand): ref base C (1/0); new base T (22/19); total (23/19) |
| 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 |
TCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGC > NZ_CP009273/4267367‑4267538
|
tCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGc < 1:590631/90‑1 (MQ=255)
ccTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCa > 2:747481/1‑90 (MQ=255)
tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc > 1:1374469/1‑90 (MQ=255)
tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc > 1:138127/1‑90 (MQ=255)
tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc < 2:465878/90‑1 (MQ=255)
tAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGtgtg < 1:624435/90‑1 (MQ=255)
aaGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGgcg > 2:483468/1‑90 (MQ=255)
aaGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGGATTGgcg > 1:1009798/1‑90 (MQ=255)
aaGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGgcg > 1:1510355/1‑90 (MQ=255)
aGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCTGTGTGGCGGTATCGgcgc < 1:1391773/90‑1 (MQ=255)
ttATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCAtt > 2:1156477/1‑90 (MQ=255)
aaaGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGa > 2:70289/1‑90 (MQ=255)
aaGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGaa < 2:614021/90‑1 (MQ=255)
aCCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAgg < 1:483468/90‑1 (MQ=255)
cccGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGt < 2:447867/90‑1 (MQ=255)
ccGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTTTGAAAGGAAAGGGtt > 2:396377/1‑90 (MQ=255)
cGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTaa > 1:1150482/1‑83 (MQ=255)
cGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTaa < 2:1150482/83‑1 (MQ=255)
gCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGa > 2:178930/1‑90 (MQ=255)
cATTAAAGCGCTGGTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGAt < 1:791212/90‑1 (MQ=255)
cATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGAt < 2:1107665/90‑1 (MQ=255)
aTTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGAtt < 2:1124488/90‑1 (MQ=255)
aTTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGAtt < 1:178930/90‑1 (MQ=255)
aaaGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTAcc < 2:933473/90‑1 (MQ=255)
aaaGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTAcc < 2:829132/90‑1 (MQ=255)
aaaGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTAcc < 2:442431/90‑1 (MQ=255)
aGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAg < 2:1234708/90‑1 (MQ=255)
gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGGTGATTACCAGTAt > 1:92357/1‑90 (MQ=255)
gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGGTGATTACCAGTAt > 2:509546/1‑90 (MQ=255)
gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGGTGATTACCAGTAt > 2:879382/1‑90 (MQ=255)
gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCCGCATTTCTATGAAAGTAAAGGGTTGATTACCAGGAt > 2:815966/1‑90 (MQ=255)
ctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATTGGCGCTGCATTTTTTTGAAAGGAAAGGGGTGGTTACCAGTATc > 1:1606515/1‑90 (MQ=255)
ctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCCTTTTTATGAAAGTAAAGGGGTGATTACCAGTATc > 1:1354148/1‑90 (MQ=255)
ccGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTTTTTGAAAGTAAAGGGGTGATTACCAGTATCCGTAACAGCg > 1:993169/1‑90 (MQ=255)
ccGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTAACGGCGCTGCATTTTTATGAAAGAAAAGGGGTGATTACCAGTATCCGTAACAGCg > 2:1602885/1‑90 (MQ=255)
cGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCgg < 2:1086028/90‑1 (MQ=255)
ggCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGGAAAGGGTTGATTACCAGTATCCGTAACAGCGGc > 2:659556/1‑90 (MQ=255)
gCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGgcgc > 2:1351506/1‑39 (MQ=39)
gCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGgcgc < 1:1351506/39‑1 (MQ=39)
aGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTTTTTGAAAGGAAAGGGGTGATTACCAGTATCCGTAACAGCGGCAATCa > 1:55024/1‑90 (MQ=255)
tGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCCTTTCTATGGAAAAAAAGGGTTGGTTTCCAGGATCCGTAACAGCGGCCATCAgc > 1:418131/1‑90 (MQ=255)
cGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAgcggc < 2:461294/90‑1 (MQ=255)
|
TCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGC > NZ_CP009273/4267367‑4267538
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGCGATATAAACGTGAT > NZ_CP009273/4267357‑4267552
|
GGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGC < SRR3722008.1078735/100‑1 (MQ=60)
GTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGC < SRR3722008.397109/100‑1 (MQ=60)
GTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGC > SRR3722008.142026/1‑100 (MQ=60)
GTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGC > SRR3722008.1411231/1‑100 (MQ=60)
cggcgaccaccgagatctacacactgcatatcgtcggcagcgtcagatgtgtataagagacaGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTG < SRR3722008.1311497/38‑1 (MQ=60)
TCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGG < SRR3722008.606584/100‑1 (MQ=60)
TAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGG < SRR3722008.641351/100‑1 (MQ=60)
ACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGGATTGGCG > SRR3722008.1037277/1‑100 (MQ=60)
ACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCG > SRR3722008.1550262/1‑100 (MQ=60)
actgcatatcgtcggcagcgtcagatgtgtataagagacaggctaaCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTA < SRR3722008.1387723/54‑1 (MQ=60)
AGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCTGTGTGGCGGTATCGGCGCTGCATTTCTA < SRR3722008.1428944/100‑1 (MQ=60)
GAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAATAAAGGGGTG > SRR3722008.1181485/1‑100 (MQ=60)
ACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACC < SRR3722008.496116/100‑1 (MQ=60)
GCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGGTGATTACCAGTAT > SRR3722008.95015/1‑100 (MQ=60)
CATTAAAGCGCTGGTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATC < SRR3722008.812774/100‑1 (MQ=60)
CATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATTGGCGCTGCATTTTTTTGAAAGGAAAGGGGTGGTTACCAGTATC > SRR3722008.1648703/1‑100 (MQ=60)
CATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCCTTTTTATGAAAGTAAAGGGGTGATTACCAGTATC > SRR3722008.1390437/1‑100 (MQ=60)
ATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCC < SRR3722008.183857/100‑1 (MQ=60)
CTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGctgtctcttatacacatctgacgctgccgacgatatgcagtgtggagatctcggtgg > SRR3722008.109564/1‑43 (MQ=60)
CTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTTTTTGAAAGTAAAGGGGTGATTACCAGTATCCGTAACAGCG > SRR3722008.1020215/1‑100 (MQ=60)
CCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTTTTTGAAAGGAAAGGGGTGATTACCAGTATCCGTAACAGCGGCAATCA > SRR3722008.56606/1‑100 (MQ=60)
CCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCCTTTCTATGGAAAAAAAGGGTTGGTTTCCAGGATCCGTAACAGCGGCCATCAGC > SRR3722008.428703/1‑100 (MQ=60)
AAATGCAGCGGTGTGGCGGTATCGGCGCTGGATTTTTATGTAAGAAAAGGGTTGATTACCAGAATCCGGAAAAGGGGCAAACAGCGGCGGTATAAACGTG > SRR3722008.168748/1‑100 (MQ=44)
AATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGCGATATAAACGTGA < SRR3722008.1187610/100‑1 (MQ=60)
ATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGGTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGCGATATAAACGTGAT > SRR3722008.1206856/1‑100 (MQ=60)
ATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGGAAAGGGGTGGTTACCAGGATCCGTAACAGCGGGAATCAGCGGCGATATAAACGGGAT > SRR3722008.128446/1‑100 (MQ=60)
ATGCAGCGGTGTGGCGGGATCCGGGCTGCATTTCTATGAAAGAAAAGGGGTGCTTACCAGGATCCGGCACAGCGGCCATCAGCGGCGATATAAACGGGAT > SRR3722008.1504682/1‑100 (MQ=40)
|
GGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGCGATATAAACGTGAT > NZ_CP009273/4267357‑4267552
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
