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 F2 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,812,807 |
(C)7→8 |
intergenic (‑50/+55) |
celF ← / ← chbR |
6‑phospho‑beta‑glucosidase/transcriptional regulator ChbR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,812,800 | 1 | . | C | 97.9%
| 153.6
/ ‑3.0
| 48 | intergenic (‑43/+62) | celF/chbR | 6‑phospho‑beta‑glucosidase/transcriptional regulator ChbR |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base C (29/18); total (30/18) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.74e-01 |
TAGCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAAT > NZ_CP009273/1812711‑1812883
|
taGCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTg > 2:1054610/1‑90 (MQ=255)
taGCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTg > 1:1318343/1‑90 (MQ=255)
gctCCCGCCACAAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑ccccc > 2:312579/1‑90 (MQ=255)
ctCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑cccccc > 2:155425/1‑90 (MQ=255)
tCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑ccccccc > 1:993759/1‑90 (MQ=255)
cccGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑cccccccc < 2:1506036/90‑2 (MQ=255)
caccaATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACa < 2:1208962/90‑1 (MQ=255)
caccaATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACa < 2:187030/90‑1 (MQ=255)
caccaATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACa < 2:1057113/90‑1 (MQ=255)
caccaATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACa < 1:661752/90‑1 (MQ=255)
tGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATc > 1:417785/1‑90 (MQ=255)
gacgacTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCCGGACATAAATAATc > 1:99730/1‑90 (MQ=255)
gacgacTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATcc > 2:742908/1‑90 (MQ=255)
acgacTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCa < 1:1212786/90‑1 (MQ=255)
aTTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGAc < 2:1314910/90‑1 (MQ=255)
aTTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGAc < 2:467438/90‑1 (MQ=255)
ggCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGatat > 1:1093431/1‑90 (MQ=255)
gCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATAtg < 2:1487790/90‑1 (MQ=255)
tAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCGACAGGACAGATATGTGAAt < 1:449116/90‑1 (MQ=255)
tAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAAt < 2:478441/90‑1 (MQ=255)
tctcCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCa > 1:1335902/1‑90 (MQ=255)
tctcCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCa < 2:976068/90‑1 (MQ=255)
ctcCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAg < 1:742908/90‑1 (MQ=255)
cccTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGt > 1:1180820/1‑90 (MQ=255)
cTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGtat > 2:314977/1‑90 (MQ=255)
tCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATaa > 2:424164/1‑90 (MQ=255)
tCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATaa > 1:773805/1‑90 (MQ=255)
aGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAGTAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTa < 2:391296/90‑1 (MQ=255)
gAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGAATAACGACTTAc > 2:698794/1‑90 (MQ=255)
aaTACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACt < 1:609947/90‑1 (MQ=255)
cTGATATCTGGCATATCTGCCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGAt > 2:98495/1‑90 (MQ=255)
cTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGat > 2:491452/1‑57 (MQ=255)
cTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGat < 1:491452/57‑1 (MQ=255)
cTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGAtt > 2:1100831/1‑90 (MQ=255)
cTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGAtt > 2:494122/1‑90 (MQ=255)
cTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGAtt < 2:331715/90‑1 (MQ=255)
cTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGAtt > 1:493677/1‑90 (MQ=255)
gATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTaa > 2:372914/1‑90 (MQ=255)
atCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGAc < 2:865555/48‑1 (MQ=255)
atCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGAc > 1:865555/1‑48 (MQ=255)
atCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAAtt > 2:1495446/1‑90 (MQ=255)
atCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAAtt > 2:837864/1‑90 (MQ=255)
atCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAAtt > 2:324408/1‑90 (MQ=255)
atCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAAtt > 2:1320633/1‑90 (MQ=255)
atCTGGCATATCCGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAAtt > 1:896812/1‑90 (MQ=255)
cTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCa > 1:394083/1‑90 (MQ=255)
cTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCa > 1:1482173/1‑90 (MQ=255)
cTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCa > 2:963434/1‑90 (MQ=255)
cTGGCATATCTG‑‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAg > 1:1219689/1‑90 (MQ=255)
ggCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGt > 2:486661/1‑90 (MQ=255)
gCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTc > 1:871051/1‑90 (MQ=255)
gCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTc > 2:1547347/1‑90 (MQ=255)
gCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTc > 2:899068/1‑90 (MQ=255)
tatCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAAt < 1:1054610/90‑1 (MQ=255)
|
TAGCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAAT > NZ_CP009273/1812711‑1812883
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ 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
GTATAGCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATTTCTTACGATAGCTCTTAGG > NZ_CP009273/1812708‑1812903
|
GTATAGCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑CCCCCCC > SRR3722078.1008210/1‑100 (MQ=60)
CCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATC > SRR3722078.422832/1‑100 (MQ=60)
CACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCCGGACATAAATAATC > SRR3722078.100904/1‑100 (MQ=60)
CACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCC < SRR3722078.669330/100‑1 (MQ=60)
ACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGAC < SRR3722078.1231853/100‑1 (MQ=60)
TTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATAT > SRR3722078.1110046/1‑100 (MQ=60)
cgtcagatgtgtataagagacagGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTG < SRR3722078.497282/77‑1 (MQ=60)
GCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCA > SRR3722078.1357319/1‑100 (MQ=60)
CATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGT > SRR3722078.1199262/1‑100 (MQ=60)
TAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCGACAGGACAGATATGTGAATTGTCAGGTAT < SRR3722078.454487/100‑1 (MQ=60)
ATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAA > SRR3722078.783810/1‑100 (MQ=60)
CTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGAC < SRR3722078.752315/100‑1 (MQ=60)
GTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATT > SRR3722078.499525/1‑100 (MQ=60)
GAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGActgtctcttatacacatctgacgctgccgacg > SRR3722078.877144/1‑68 (MQ=60)
GAATACTGATATCTGGCATATCCGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATT > SRR3722078.908856/1‑100 (MQ=60)
AATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTC < SRR3722078.616989/100‑1 (MQ=60)
ATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCA > SRR3722078.398871/1‑100 (MQ=60)
ATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCA > SRR3722078.1506342/1‑100 (MQ=60)
ATACTGATATCTGGCATATCTG‑‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAG > SRR3722078.1238886/1‑100 (MQ=60)
CTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTC > SRR3722078.882724/1‑100 (MQ=60)
GGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATTTCTTA > SRR3722078.215835/1‑100 (MQ=60)
TATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATTTCTTACGAT < SRR3722078.1070449/100‑1 (MQ=60)
CCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATTTCTTACGATAGCTCTTAGG < SRR3722078.429274/100‑1 (MQ=60)
CCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATTTCTTACGATAGCTCTTAGG < SRR3722078.293444/100‑1 (MQ=60)
|
GTATAGCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATTTCTTACGATAGCTCTTAGG > NZ_CP009273/1812708‑1812903
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
