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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,670,359 |
T→C |
G454G (GGA→GGG) |
yphE ← |
sugar ABC transporter ATP‑binding protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,670,359 | 0 | T | C | 80.0%
| 41.6
/ 10.2
| 25 | G454G (GGA→GGG) | yphE | sugar ABC transporter ATP‑binding protein |
| Reads supporting (aligned to +/- strand): ref base T (5/0); new base C (13/7); total (18/7) |
| Fisher's exact test for biased strand distribution p-value = 2.74e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.23e-01 |
CGTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGC > NZ_CP009273/2670283‑2670440
|
cgtgcTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGcagcca < 1:533507/90‑1 (MQ=255)
gtgcTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGcagccag > 2:700788/1‑90 (MQ=255)
gcTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCt > 1:264606/1‑90 (MQ=255)
aaCAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACa > 1:427888/1‑90 (MQ=255)
aaCAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACgg > 2:561524/1‑87 (MQ=255)
aaCAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACgg < 1:561524/87‑1 (MQ=255)
gATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACg > 2:46420/1‑90 (MQ=255)
gATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACg > 1:122818/1‑90 (MQ=255)
gATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACg > 1:497014/1‑90 (MQ=255)
gATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACg > 2:319934/1‑90 (MQ=255)
gATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACg > 2:615660/1‑90 (MQ=255)
gATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACg > 1:183609/1‑90 (MQ=255)
gATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACg > 2:720398/1‑90 (MQ=255)
tGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGt < 1:434729/90‑1 (MQ=255)
cAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGttt < 1:720398/90‑1 (MQ=255)
aGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGcagcca > 1:65555/1‑58 (MQ=255)
aGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGcagcca < 2:65555/58‑1 (MQ=255)
tCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGAcgccg > 2:365183/1‑90 (MQ=255)
aCTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCcgcg > 1:672936/1‑90 (MQ=255)
gaTAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGAcgcc > 2:407968/1‑81 (MQ=255)
gaTAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGAcgcc < 1:407968/81‑1 (MQ=255)
tAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCt > 1:619589/1‑90 (MQ=255)
tAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCt > 1:182612/1‑90 (MQ=255)
cacGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAg < 1:700788/90‑1 (MQ=255)
acGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGc > 1:145338/1‑90 (MQ=255)
|
CGTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGC > NZ_CP009273/2670283‑2670440
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ 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
AACGTGCCGTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGCAACAAAATC > NZ_CP009273/2670276‑2670449
|
AACGTGCCGTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCT > SRR3722079.266825/1‑100 (MQ=60)
CGTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGAC < SRR3722079.538497/100‑1 (MQ=60)
GTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACA > SRR3722079.431586/1‑100 (MQ=60)
GTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACG > SRR3722079.123825/1‑100 (MQ=60)
GTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACG > SRR3722079.185212/1‑100 (MQ=60)
GTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACG > SRR3722079.501441/1‑100 (MQ=60)
AATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGT < SRR3722079.566978/100‑1 (MQ=60)
TGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTG < SRR3722079.438490/100‑1 (MQ=60)
GTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACctgtctcttatacacatctccg > SRR3722079.66093/1‑78 (MQ=60)
CAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCGTCGATA < SRR3722079.728093/100‑1 (MQ=60)
CCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCG > SRR3722079.679986/1‑100 (MQ=60)
TTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGC < SRR3722079.411441/100‑1 (MQ=60)
TCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCT > SRR3722079.184209/1‑100 (MQ=60)
TCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCT > SRR3722079.625888/1‑100 (MQ=60)
GATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGC > SRR3722079.146592/1‑100 (MQ=60)
CACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGCAACAAAATC < SRR3722079.708206/100‑1 (MQ=60)
|
AACGTGCCGTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGCAACAAAATC > NZ_CP009273/2670276‑2670449
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
