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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
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 | 100.0%
| 44.7
/ NA
| 15 | intergenic (‑43/+62) | celF/chbR | 6‑phospho‑beta‑glucosidase/transcriptional regulator ChbR |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (7/8); total (7/8) |
GCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTC > NZ_CP009273/1812716‑1812880
|
gctCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑ccccc > 1:304376/1‑90 (MQ=255)
gctCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑ccccc > 2:482611/1‑90 (MQ=255)
tCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑ccccccc > 1:86168/1‑90 (MQ=255)
tCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑ccccccc > 2:33313/1‑90 (MQ=255)
tCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑ccccccc > 2:30373/1‑90 (MQ=255)
cccGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑cccccccc < 2:46982/90‑2 (MQ=255)
cccGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑cccccccc < 1:5529/90‑2 (MQ=255)
gCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑ccccccccgga < 2:455254/90‑5 (MQ=255)
gacgacTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑cccccccc > 2:48886/1‑74 (MQ=255)
gacgacTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑cccccccc < 1:48886/75‑2 (MQ=255)
ttttAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAAc < 2:12577/90‑1 (MQ=255)
aTTTCTGGCTCATAATTTCCCCCTTCAGTACAGAATCCTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGAc < 1:350317/90‑1 (MQ=255)
tctcCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCa < 2:420373/90‑1 (MQ=255)
ctcCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTc < 2:575828/88‑1 (MQ=255)
ctcCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTc > 1:575828/1‑88 (MQ=255)
cTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGAtt > 1:1724/1‑90 (MQ=255)
gATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTaa > 1:582146/1‑90 (MQ=255)
atCTGGCATATCTGCCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAAt > 1:190792/1‑90 (MQ=255)
atCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATAtgtg > 2:135513/1‑57 (MQ=255)
atCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATAtgtg < 1:135513/57‑1 (MQ=255)
atCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAAtt < 2:425745/90‑1 (MQ=255)
atCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAAtt > 1:380212/1‑90 (MQ=255)
cTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAg > 2:321589/1‑64 (MQ=255)
cTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAg < 1:321589/64‑1 (MQ=255)
gCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTc < 2:104032/90‑1 (MQ=255)
|
GCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTC > NZ_CP009273/1812716‑1812880
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ 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 > SRR3722111.87225/1‑100 (MQ=60)
gacagCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAAT < SRR3722111.49477/95‑1 (MQ=60)
CCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAAT < SRR3722111.5598/100‑1 (MQ=60)
ATTTCTGGCTCATAATTTCCCCCTTCAGTACAGAATCCTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGA < SRR3722111.355071/100‑1 (MQ=60)
CTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAG > SRR3722111.584868/1‑100 (MQ=60)
cgtcagatgtgtataagagacagGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGG < SRR3722111.137219/77‑1 (MQ=60)
tgtgtataagagacagATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGAC < SRR3722111.325854/84‑1 (MQ=60)
CTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATctgtctcttatacacatctgacgctgccgacgaatgtcaatgtgtagt > SRR3722111.269881/1‑52 (MQ=60)
GTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATT > SRR3722111.1747/1‑100 (MQ=60)
ACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAA > SRR3722111.591274/1‑100 (MQ=60)
GAATACTGATATCTGGCATATCTGCCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAAT > SRR3722111.193176/1‑100 (MQ=60)
GAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATT > SRR3722111.385671/1‑100 (MQ=60)
ATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAActgtctcttatacacatctgacgctgccgacgaatgtcaatgtgtagatctcggtggt > SRR3722111.188536/1‑42 (MQ=60)
CCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATTTCTTACGATAGCTCTTAGG < SRR3722111.30739/100‑1 (MQ=60)
CCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATTTCTTACGATAGCTCTTAGG < SRR3722111.78936/100‑1 (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 < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
