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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
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 | 97.1%
| 116.2
/ ‑3.8
| 34 | intergenic (‑43/+62) | celF/chbR | 6‑phospho‑beta‑glucosidase/transcriptional regulator ChbR |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (18/15); total (18/16) |
| Fisher's exact test for biased strand distribution p-value = 4.71e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TAGCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TG‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGT > NZ_CP009273/1812711‑1812879
|
taGCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑Tg > 1:158992/1‑90 (MQ=255)
tCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TG‑ccccccc > 2:286081/1‑90 (MQ=255)
tCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TG‑ccccccc > 2:515075/1‑90 (MQ=255)
cccGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TG‑cccccccc < 1:15590/90‑2 (MQ=255)
cccGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TG‑cccccccc < 1:65595/90‑2 (MQ=255)
cGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TG‑ccccccccgg < 1:702744/90‑4 (MQ=255)
cGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TG‑ccccccccgg < 1:297310/90‑4 (MQ=255)
caccaATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACa < 2:205065/90‑1 (MQ=255)
caccaATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACa < 2:158992/90‑1 (MQ=255)
gTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAaataat < 1:97778/90‑1 (MQ=255)
gTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAaataat < 1:616535/90‑1 (MQ=255)
acgacTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCa < 1:342695/90‑1 (MQ=255)
ttttAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAAc < 1:435456/90‑1 (MQ=255)
ttttAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAAc < 2:447013/90‑1 (MQ=255)
ttttAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAAc < 1:515075/90‑1 (MQ=255)
tttAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACa > 1:380864/1‑90 (MQ=255)
aTTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGAc < 1:286081/90‑1 (MQ=255)
aTTTCTGGCCCATAATTTCTCCCTTCAGTACAGAATACTGAAAACTGGCCTATCTTC‑CCCCCCCGGACATAAATAATCCAGCAACAGGAc < 1:529164/90‑1 (MQ=255)
tctcCCTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCa > 2:274269/1‑90 (MQ=255)
tCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATaa < 1:354998/90‑1 (MQ=255)
aGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTa < 2:366042/90‑1 (MQ=255)
gAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTAc > 2:451344/1‑90 (MQ=255)
gAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTAc > 1:447428/1‑90 (MQ=255)
aTACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTg > 1:382194/1‑90 (MQ=255)
cTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAAc > 2:723962/1‑48 (MQ=255)
cTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAAc < 1:723962/48‑1 (MQ=39)
cTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATAtg < 2:7917/60‑1 (MQ=255)
cTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATAtg > 1:7917/1‑60 (MQ=255)
cTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGAtt > 2:309704/1‑90 (MQ=255)
cTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGAtt > 1:475574/1‑90 (MQ=255)
cTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGAtt > 2:610690/1‑90 (MQ=255)
cTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGAtt > 1:288924/1‑90 (MQ=255)
gATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTaa > 1:661773/1‑90 (MQ=255)
gATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTaa > 2:354922/1‑90 (MQ=255)
atCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAAtt > 1:63969/1‑90 (MQ=255)
atCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAAtt > 2:693582/1‑90 (MQ=255)
tCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTc < 2:634614/90‑1 (MQ=255)
cTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGat > 1:50961/1‑50 (MQ=255)
cTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGat < 2:50961/50‑1 (MQ=255)
cTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGAAATGTGAATTGTCAGGTATAACGACTTAATGATTAAATTCa > 1:186698/1‑90 (MQ=255)
ggCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGt > 1:487055/1‑90 (MQ=255)
|
TAGCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TG‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGT > NZ_CP009273/1812711‑1812879
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ 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
CCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TG‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATTTCTTACGAT > NZ_CP009273/1812719‑1812893
|
CCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAAT < SRR3722073.15987/100‑1 (MQ=60)
CCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAAT < SRR3722073.67130/100‑1 (MQ=60)
CGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAA < SRR3722073.716987/100‑1 (MQ=60)
CGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAA < SRR3722073.303603/100‑1 (MQ=60)
CCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATC < SRR3722073.551350/100‑1 (MQ=60)
AGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACA > SRR3722073.388966/1‑100 (MQ=60)
GTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAG < SRR3722073.99923/100‑1 (MQ=60)
GTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAG < SRR3722073.629356/100‑1 (MQ=60)
ACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGAC < SRR3722073.349959/100‑1 (MQ=60)
cgtcggcagcgtcagatgtgtataagagacagGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATA < SRR3722073.738578/68‑1 (MQ=60)
TTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATA < SRR3722073.444768/100‑1 (MQ=60)
TTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATA < SRR3722073.525923/100‑1 (MQ=60)
ATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGA < SRR3722073.292143/100‑1 (MQ=60)
ATTTCTGGCCCATAATTTCTCCCTTCAGTACAGAATACTGAAAACTGGCCTATCTTC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGA < SRR3722073.540240/100‑1 (MQ=60)
CTTCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTAC > SRR3722073.456982/1‑100 (MQ=60)
TCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTG < SRR3722073.362508/100‑1 (MQ=60)
TCAGTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTG > SRR3722073.390319/1‑100 (MQ=60)
GTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCActgtctcttatacacatctg > SRR3722073.8118/1‑80 (MQ=60)
GTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATT > SRR3722073.295037/1‑100 (MQ=60)
GTACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATT > SRR3722073.485704/1‑100 (MQ=60)
ACAGAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAA > SRR3722073.675336/1‑100 (MQ=60)
GAATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATT > SRR3722073.65470/1‑100 (MQ=60)
ATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGctgtctcttatacacatctgacgctgccga > SRR3722073.52159/1‑70 (MQ=60)
ATACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGAAATGTGAATTGTCAGGTATAACGACTTAATGATTAAATTCA > SRR3722073.190362/1‑100 (MQ=60)
ACTGATATCTGGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGT > SRR3722073.497406/1‑100 (MQ=60)
GGCATATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGGATAACGACTTACTGATTAAATTCAGTCAATTTCTTA > SRR3722073.291590/1‑100 (MQ=60)
TATC‑TGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATTTCTTACGAT > SRR3722073.593704/1‑100 (MQ=60)
|
CCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATC‑TG‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATTTCTTACGAT > NZ_CP009273/1812719‑1812893
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
