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 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,276,251 |
Δ1 bp |
coding (932/3744 nt) |
narG → |
nitrate reductase subunit alpha |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,276,249 | 0 | G | . | 95.0%
| 75.6
/ ‑2.8
| 20 | coding (930/3744 nt) | narG | nitrate reductase subunit alpha |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base . (7/12); total (7/13) |
| 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 |
CACACCAGACTACGCTGAAATCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGATGGGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCGACTATGTGCGTCGCTACACCGACATGCC > NZ_CP009273/1276162‑1276332
|
cacaCCAGACTACGCTGAAATCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGATggc < 2:52746/90‑2 (MQ=255)
cacaCCAGACTACGCTGAAATCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGATggc < 2:1188074/90‑2 (MQ=255)
cacaCCAGACTACGCTGAAATCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGATggc < 1:579487/90‑2 (MQ=255)
aCGCTGAAATCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAAtgct > 1:407580/1‑90 (MQ=255)
aCGCTGAAATCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAAtgct > 1:643066/1‑90 (MQ=255)
aCGCTGAAATCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAAtgct > 1:734669/1‑90 (MQ=255)
aaaCTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCAcc < 2:234752/90‑1 (MQ=255)
gtgCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGAc < 2:381663/90‑1 (MQ=255)
cTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCaa < 1:985387/90‑1 (MQ=255)
tggctggcACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGATggc < 2:1179212/50‑2 (MQ=255)
tggctggcACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGATggc > 1:1179212/1‑49 (MQ=255)
tggctggcACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGcc < 1:565291/90‑1 (MQ=255)
gctggcACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAg < 2:1085585/90‑1 (MQ=255)
ggcACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTAt > 1:554954/1‑90 (MQ=255)
cGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCAc < 2:1079249/90‑1 (MQ=255)
gAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCAcc < 1:1098968/90‑1 (MQ=255)
gggCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGcc < 2:787084/73‑1 (MQ=255)
gggCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGcc > 1:787084/1‑73 (MQ=255)
gggCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCGACTAt > 2:1012427/1‑90 (MQ=255)
aCCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCCCCTCGACAACCCAAGCCAGTATTTCACCGACTATGTGc < 2:681769/90‑1 (MQ=255)
ccGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGcc > 2:1152414/1‑68 (MQ=255)
ccGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGcc < 1:1152414/68‑1 (MQ=255)
tGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCGACTATGTGCGTCGc < 1:395787/90‑1 (MQ=255)
ggCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCGACTATGTGCGTCGCTac < 1:890594/90‑1 (MQ=255)
tGGCGA‑GGGCCACGTAATGCTGCGTGAATCCCCCCCCGACAACCCAAGCCAGTATTTCACCGACTATGTGCGTCGCTACACCGACATGcc < 1:993896/90‑1 (MQ=255)
|
CACACCAGACTACGCTGAAATCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGATGGGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCGACTATGTGCGTCGCTACACCGACATGCC > NZ_CP009273/1276162‑1276332
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 30 ≤ 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
CACACCAGACTACGCTGAAATCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGATGGGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCGACTATGTGCGTCGCTACACCGACATGCCGATGCTGGTGA > NZ_CP009273/1276162‑1276343
|
CACACCAGACTACGCTGAAATCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGC < SRR3722089.586409/100‑1 (MQ=60)
ACACCAGACTACGCTGAAATCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCT > SRR3722089.744255/1‑100 (MQ=60)
ACACCAGACTACGCTGAAATCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCT > SRR3722089.651284/1‑100 (MQ=60)
ACACCAGACTACGCTGAAATCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCT > SRR3722089.412513/1‑100 (MQ=60)
tacactaagatggtcgtcggcagcgtcagatgtgtataagagacaGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCC < SRR3722089.942511/55‑1 (MQ=60)
GTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCctgtctcttatacacatctgacgctgccga > SRR3722089.1197178/1‑70 (MQ=60)
ATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTAT > SRR3722089.561398/1‑100 (MQ=60)
CTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTT < SRR3722089.999992/100‑1 (MQ=60)
tataagagacaGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCAC < SRR3722089.1169955/89‑1 (MQ=60)
TGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCAC < SRR3722089.571938/100‑1 (MQ=60)
CACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCtgtctc > SRR3722089.797872/1‑94 (MQ=60)
GAAACAGGGCACCGATGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCGACTATGTGC < SRR3722089.1115576/100‑1 (MQ=60)
TGCGGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCGACTATGTGCGTCGCTACACCGACA < SRR3722089.400605/100‑1 (MQ=60)
GGCAATGGCGCTGGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCGACTATGTGCGTCGCTACACCGACATGC < SRR3722089.903457/100‑1 (MQ=60)
TGGCGA‑GGGCCACGTAATGCTGCGTGAATCCCCCCCCGACAACCCAAGCCAGTATTTCACCGACTATGTGCGTCGCTACACCGACATGCCGATGCTGGTG < SRR3722089.1008657/100‑1 (MQ=60)
GGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCGACTATGTGCtgtctcttatacacatctgacgctgccgac > SRR3722089.843455/1‑70 (MQ=60)
GGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCGACTATGTGCGTCGCTACACCGACATGCCGATGCTGGTGA > SRR3722089.560086/1‑100 (MQ=60)
GGCGAT‑GGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCGACTATGTGCGTCGCTACACCGACATGCCGATGCTGGTGA > SRR3722089.937943/1‑100 (MQ=60)
|
CACACCAGACTACGCTGAAATCGCCAAACTGTGCGATCTGTGGCTGGCACCGAAACAGGGCACCGATGCGGCAATGGCGCTGGCGATGGGCCACGTAATGCTGCGTGAATTCCACCTCGACAACCCAAGCCAGTATTTCACCGACTATGTGCGTCGCTACACCGACATGCCGATGCTGGTGA > NZ_CP009273/1276162‑1276343
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
