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 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,818,674 |
A→C |
L174R (CTG→CGG) |
ves ← |
environmental stress‑induced protein Ves |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,818,674 | 0 | A | C | 100.0%
| 71.9
/ NA
| 21 | L174R (CTG→CGG) | ves | environmental stress‑induced protein Ves |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (12/9); total (12/9) |
TTGTAAGCCGCTGCTTTCCGGTAACTATGAAATTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACAGTTTACCTTGCGGTTGTAAAAGCCGCAGGGTGTGCCTGCCATCGAACCAGCACGCGCCCTGGTC > NZ_CP009273/1818587‑1818738
|
ttGTAAGCCGCTGCTTTCCGGTAACTATGAAATTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGGACAACCGt > 1:704972/1‑90 (MQ=255)
ttGTAAGCCGCTGCTTTCCGGTAACTATGAAATTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGt > 1:571687/1‑90 (MQ=255)
tGTAAGCCGCTGCTTTCCGGTAACTATGAAATTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGtt < 1:305767/90‑1 (MQ=255)
tAAGCCGCTGCTTTCCGGTAACTATGAAATTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTa > 1:743236/1‑90 (MQ=255)
aGCTGCTGCTTTCCGGTAACTATGAAATTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTAcc > 2:601085/1‑90 (MQ=255)
gctgctTTCCGGTAACTATGAAATTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGc < 2:362454/90‑1 (MQ=255)
ttCCGGTAACTATGAAATTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGCGGTTGt > 2:60977/1‑90 (MQ=255)
cTATGAAATTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGCGGTTGTAAAAGCCGc < 2:221830/90‑1 (MQ=255)
tATGAAATTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGCGGTTGTAAAAGCCGCa > 1:364089/1‑90 (MQ=255)
aaTTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGCGGTTGTAAAAGCCGCAGGgtg > 2:566176/1‑90 (MQ=255)
aaTTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGCGGTTGTAAAAGCCGCAGGgtg > 2:503242/1‑90 (MQ=255)
aCTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGCGGTTGTAAAAGCCGCAGGGTGtgcc > 1:572382/1‑90 (MQ=255)
cTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGCGGTTGTAAAAGCCGCAGGGTGtgcct < 1:387099/90‑1 (MQ=255)
tGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGCGGTTGTAAAAGCCGCAGGGTGTGCCTGCCATCg > 2:870754/1‑90 (MQ=255)
tGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGCGGTTGTAAAAGCCGCAGGGTGTGCCTGCCATCg > 1:360217/1‑90 (MQ=255)
gCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGCGGTTGTAAAAGCCGCAGGGGGTGCCTGCCATCGAACCAGc > 1:745607/1‑90 (MQ=255)
aTGCCCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGCGGTTGTAAAAGCCGCAGGGTGTGCCTGCCATCGAACCAGCAcgc < 1:304921/90‑1 (MQ=255)
aTGACCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGCGGTTGTAAAAGCCGCAGGGTGTGCCTGCCATCGAACCAGCAcgc < 1:912640/90‑1 (MQ=255)
ccAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGCGGTTGTAAAAGCCGCAGGGTGTGCCTGCCATCGAACCAGCACGCGccc < 2:360217/90‑1 (MQ=255)
ccAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGCGGTTGTAAAAGCCGCAGGGTGTGCCTGCCATCGAACCAGCACGCGccc < 2:201809/90‑1 (MQ=255)
gAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGCGGTTGTAAAAGCCGCAGGGTGTGCCTGCCATCGAACCAGCACGCGCCCTGGTc < 2:364089/90‑1 (MQ=255)
|
TTGTAAGCCGCTGCTTTCCGGTAACTATGAAATTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACAGTTTACCTTGCGGTTGTAAAAGCCGCAGGGTGTGCCTGCCATCGAACCAGCACGCGCCCTGGTC > NZ_CP009273/1818587‑1818738
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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
TATAAAATTCTTTGTAAGCCGCTGCTTTCCGGTAACTATGAAATTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACAGTTTACCTTGCGGTTGTAAAAGCCGCAGGGTGTGCCTGCCATCGAACCAGCACGCGCCCTGGTCGGTAGTGAGCAATTTATCGCCCAGTTGCCACGCCC > NZ_CP009273/1818576‑1818773
|
ataagagacagTTGTAAGCCGCTGCTTTCCGGTAACTATGAAATTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCG < SRR3722072.904405/89‑1 (MQ=60)
ataagagacagTTGTAAGCCGCTGCTTTCCGGTAACTATGAAATTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCG < SRR3722072.872821/89‑1 (MQ=60)
ATAAAATTCTTTGTAAGCCGCTGCTTTCCGGTAACTATGAAATTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGGACAACCGT > SRR3722072.717546/1‑100 (MQ=60)
ATAAAATTCTTTGTAAGCCGCTGCTTTCCGGTAACTATGAAATTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGT > SRR3722072.581903/1‑100 (MQ=60)
AAATTCTTTGTAAGCCGCTGCTTTCCGGTAACTATGAAATTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTA > SRR3722072.756387/1‑100 (MQ=60)
ataatcggacgtctcgtgggctcggagatgtgtataagagacagACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACC < SRR3722072.90081/56‑1 (MQ=60)
TGTAAGCCGCTGCTTTCCGGTAACTATGAAATTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGCGG < SRR3722072.311062/100‑1 (MQ=60)
TTCCGGTAACTATGAAATTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGCGGTTGTAAAAGCCGCA > SRR3722072.370547/1‑100 (MQ=60)
CTATGAAATTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGCGGTTGTAAAAGCCGCAGGGTGTGCC > SRR3722072.582610/1‑100 (MQ=60)
TTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGCGGTTGTAAAAGCCGCAGGGTGTGCCTGCCATCG > SRR3722072.366604/1‑100 (MQ=60)
CTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGCGGTTGTAAAAGCCGCAGGGTGTGCCTGCCATCGAAC < SRR3722072.394034/100‑1 (MQ=60)
ACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGCGGTTGTAAAAGCCGCAGGGGGTGCCTGCCATCGAACCAGC > SRR3722072.758794/1‑100 (MQ=60)
ATGCCCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGCGGTTGTAAAAGCCGCAGGGTGTGCCTGCCATCGAACCAGCACGCGCCCTGGTCG < SRR3722072.310205/100‑1 (MQ=60)
ATGACCAGCGAGCCAGTTGATTTCACTGAACAACCGTTTACCTTGCGGTTGTAAAAGCCGCAGGGTGTGCCTGCCATCGAACCAGCACGCGCCCTGGTCG < SRR3722072.928324/100‑1 (MQ=60)
CTGAACAACCGTTTACCTTGCGGTTGTAAAAGCCGCAGGGTGTGCCTGCCATCGAACCAGCACGCGCCCTGGTCGGTAGTGAGCctgtctcttatacaca > SRR3722072.669784/1‑84 (MQ=60)
GAACAACCGTTTACCTTGCGGTTGTAAAAGCCGCAGGGTGTGCCTGCCATCGAACCAGCACGCGCCCTGGTCGGTAGTGAGCAATTTATCGCCCAGTTGC > SRR3722072.497215/1‑100 (MQ=60)
ACCGTTTACCTTGCGGTTGTAAAAGCCGCAGGGTGTGCCTGCCATCGAACCAGCACGCGCCCTGGTCGGTAGTGAGCAATTTATCGCCCAGTTGCCACGC > SRR3722072.185098/1‑100 (MQ=60)
CCGTTTACCTTGCGGTTGTAAAAGCCGCAGGGTGTGCCTGCCATCGAACCAGCACGCGCCCTGGTCGGTAGTGAGCAATTTATCGCCCAGTTGCCACGCT > SRR3722072.895389/1‑100 (MQ=60)
CGTTTACCTTGCGGTTGTAAAAGCCGCAGGGTGTGCCTGCCATCGAACCAGCACGCGCCCTGGTCGGTAGTGAGCctgtctcttatacacatctccgagc > SRR3722072.90327/1‑75 (MQ=60)
|
TATAAAATTCTTTGTAAGCCGCTGCTTTCCGGTAACTATGAAATTACTGAACTTGATCCGGCGAATGACCAGCGAGCCAGTTGATTTCACTGAACAACAGTTTACCTTGCGGTTGTAAAAGCCGCAGGGTGTGCCTGCCATCGAACCAGCACGCGCCCTGGTCGGTAGTGAGCAATTTATCGCCCAGTTGCCACGCCC > NZ_CP009273/1818576‑1818773
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
