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 I205 R1
|
220 |
17.5 |
961422 |
97.1% |
933540 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,796,543 |
G→C |
G95G (GGC→GGG) |
thrS ← |
threonine‑‑tRNA ligase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,796,543 | 0 | G | C | 100.0%
| 62.3
/ NA
| 21 | G95G (GGC→GGG) | thrS | threonine‑‑tRNA ligase |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (6/15); total (6/15) |
ATCCGCTTCTCGAGTGCTTCGACATCTTCCTGGGTTAACGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGGCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATGA > NZ_CP009273/1796457‑1796619
|
aTCCGCTTCTCGAGTGCTTCGACATCTTCCTGGGTTAACGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCg > 2:226121/1‑90 (MQ=255)
cTTCTCGAGTGCTTCGACATCTTCCTGGGTTAACGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGc < 1:32941/90‑1 (MQ=255)
tctcGAGTGCTTCGACATCTTCCTGGGTTAACGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCa > 2:349910/1‑90 (MQ=255)
cTTCCTGGGTTAACGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCaaa < 2:282496/90‑1 (MQ=255)
gTTAACGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTa > 1:420195/1‑90 (MQ=255)
cGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATcgc < 1:178822/90‑1 (MQ=255)
tGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCCGCCAAAGTTGTTTAATCGCGt < 2:325650/90‑1 (MQ=255)
gCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAgt > 1:380517/1‑76 (MQ=255)
gCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAgt < 2:380517/76‑1 (MQ=255)
gCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTg < 2:126843/90‑1 (MQ=255)
ggTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGcc < 1:326341/90‑1 (MQ=255)
aaCGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTg < 1:420941/90‑1 (MQ=255)
gtcgtAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTgcgc < 1:190447/90‑1 (MQ=255)
gtcgtAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTgcgc < 2:63581/90‑1 (MQ=255)
gtcgtAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTgcgc < 2:356110/90‑1 (MQ=255)
agtAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGcac < 2:314367/89‑1 (MQ=255)
gtAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGcaca > 1:95673/1‑90 (MQ=255)
gTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTg > 1:475359/1‑60 (MQ=255)
gTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTg < 2:475359/60‑1 (MQ=255)
tGTCAATAACCGGCCCGCTTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATGa < 1:315598/90‑1 (MQ=255)
tGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATGa < 2:95673/90‑1 (MQ=255)
|
ATCCGCTTCTCGAGTGCTTCGACATCTTCCTGGGTTAACGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGGCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATGA > NZ_CP009273/1796457‑1796619
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ 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
CTTCTCGAGTGCTTCGACATCTTCCTGGGTTAACGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGGCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATGATCTCCAGACCT > NZ_CP009273/1796462‑1796630
|
CTTCTCGAGTGCTTCGACATCTTCCTGGGTTAACGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTA < SRR3722087.33209/100‑1 (MQ=60)
ATCTTCCTGGGTTAACGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTA > SRR3722087.425086/1‑100 (MQ=60)
GGGTTAACGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCtgt > SRR3722087.384900/1‑97 (MQ=60)
CGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAAC < SRR3722087.180420/100‑1 (MQ=60)
GGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTG < SRR3722087.329890/100‑1 (MQ=60)
GATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACA > SRR3722087.96590/1‑100 (MQ=60)
AACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAG < SRR3722087.425840/100‑1 (MQ=60)
GTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGA < SRR3722087.192124/100‑1 (MQ=60)
AATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGctgtctcttatacacatctc > SRR3722087.480889/1‑80 (MQ=60)
TGTCAATAACCGGCCCGCTTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATGATCTCCAGACC < SRR3722087.318963/100‑1 (MQ=60)
TGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATGATCTCCAGACC < SRR3722087.378305/100‑1 (MQ=60)
GTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATGATCTCCAGACCT > SRR3722087.192628/1‑100 (MQ=60)
GTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATGATCTCCAGACCT > SRR3722087.365679/1‑100 (MQ=60)
|
CTTCTCGAGTGCTTCGACATCTTCCTGGGTTAACGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGGCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATGATCTCCAGACCT > NZ_CP009273/1796462‑1796630
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
