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 I231 R1
|
218 |
12.8 |
703680 |
97.2% |
683976 |
86.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,527,151 |
T→C |
Q87Q (CAA→CAG) |
nanS ← |
9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,527,151 | 0 | T | C | 100.0%
| 58.6
/ NA
| 18 | Q87Q (CAA→CAG) | nanS | 9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (10/8); total (10/8) |
TGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTTTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTAA > NZ_CP009273/4527079‑4527236
|
tGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCag < 1:304743/90‑1 (MQ=255)
gAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGAt < 1:88110/90‑1 (MQ=255)
tGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAAc < 2:172542/90‑1 (MQ=255)
gCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCa < 1:101483/90‑1 (MQ=255)
cGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACa < 1:178951/90‑1 (MQ=255)
cGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACa > 1:286343/1‑90 (MQ=255)
tGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATc > 1:284242/1‑90 (MQ=255)
atatGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCgtgt < 2:122628/90‑1 (MQ=255)
atatGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCgtgt > 2:271647/1‑90 (MQ=255)
tGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGa > 2:324002/1‑54 (MQ=255)
tGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGa < 1:324002/54‑1 (MQ=255)
gTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGt > 1:61602/1‑90 (MQ=255)
tGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTg > 2:96791/1‑90 (MQ=255)
gCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGa > 2:175240/1‑90 (MQ=255)
ccTGGCCAACGGTGCCGTACTGCGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAg > 2:182514/1‑90 (MQ=255)
gtgtCTGATGATTCGTTGCCAGAGGATGGTGATAAcc > 2:14454/1‑37 (MQ=38)
gtgtCTGATGATTCGTTGCCAGAGGATGGTGATAAcc < 1:14454/37‑1 (MQ=38)
gtgtCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTaa > 1:12828/1‑90 (MQ=255)
|
TGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTTTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTAA > NZ_CP009273/4527079‑4527236
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTTTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTAAAGTGACATGGCG > NZ_CP009273/4527056‑4527248
|
CAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGAT < SRR3722116.221753/100‑1 (MQ=60)
TGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGA < SRR3722116.309231/100‑1 (MQ=60)
cagcgtcagatgtgtataagagacagCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAAC < SRR3722116.328823/74‑1 (MQ=60)
GAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCAT < SRR3722116.89201/100‑1 (MQ=60)
acagccaacttcgtcggcagcgtcagatgtgtataagagacaGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCC < SRR3722116.14648/58‑1 (MQ=60)
GCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAAC < SRR3722116.102728/100‑1 (MQ=60)
CAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACA > SRR3722116.290519/1‑100 (MQ=60)
GTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATC > SRR3722116.288375/1‑100 (MQ=60)
CGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGC < SRR3722116.181140/100‑1 (MQ=60)
GCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGT > SRR3722116.62361/1‑100 (MQ=60)
ataagagacagGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAAGCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAA < SRR3722116.135957/89‑1 (MQ=60)
GTGCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTAA > SRR3722116.12998/1‑100 (MQ=60)
GCCGTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTAAAG > SRR3722116.241340/1‑100 (MQ=60)
GTACTGTGTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTAAAGTGA > SRR3722116.181278/1‑100 (MQ=60)
GTCTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCtgtctcttatacacatc > SRR3722116.139146/1‑83 (MQ=60)
|
CAACACGGAACGATAAGAATCCCTGCATTATCAGGAATGAAGGGCAGTAATTTCCGTGCAATATGCAGTGCCTGGCCAACGGTGCCGTACTGTGTTTGATGATTCGTTGCCAGAGGATGGTGATAACCCTGCATATCCTGAACATCGTGTGGGCAGTGAGTCAGTGGAATAATGTCGTTAAAGTGACATGGCG > NZ_CP009273/4527056‑4527248
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
