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 |
1,153,703 |
A→T |
I127F (ATC→TTC) |
ptsG → |
PTS glucose transporter subunit IIBC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,153,703 | 0 | A | T | 83.3%
| 43.6
/ 2.9
| 18 | I127F (ATC→TTC) | ptsG | PTS glucose transporter subunit IIBC |
| Reads supporting (aligned to +/- strand): ref base A (0/3); new base T (6/9); total (6/12) |
| Fisher's exact test for biased strand distribution p-value = 5.15e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.01e-01 |
CCACTGGTACTGCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGATCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTAAACGCTTTGTGCCGATC > NZ_CP009273/1153616‑1153789
|
ccACTGGTACTGCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGATc < 1:242238/90‑1 (MQ=255)
aCTGGTACTGCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGATCGc < 2:555851/90‑1 (MQ=255)
cTGGTACTGCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCa > 1:42303/1‑90 (MQ=255)
tGGTACTGCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAg < 2:42303/90‑1 (MQ=255)
tGCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACa < 1:341493/90‑1 (MQ=255)
gctgAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGt > 1:138214/1‑90 (MQ=255)
gaaATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTAc < 2:317354/90‑1 (MQ=255)
gaaATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTAc < 2:30166/90‑1 (MQ=255)
tCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTa > 2:711938/1‑90 (MQ=255)
ctAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGc < 2:480110/90‑1 (MQ=255)
ctAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGc < 2:667333/90‑1 (MQ=255)
ccTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGa > 1:360871/1‑90 (MQ=255)
ggCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGcttc > 1:288721/1‑90 (MQ=255)
cTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGcc > 2:18627/1‑90 (MQ=255)
gggATTATCTCCGGTGCGATCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTaaa < 1:428193/90‑1 (MQ=255)
tATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTAAACGCtt < 1:622836/90‑1 (MQ=255)
ccGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTAAACGCTTTGTGc < 2:288721/90‑1 (MQ=255)
gCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTAAACGCTTTGTGCCGATc < 1:709608/90‑1 (MQ=255)
|
CCACTGGTACTGCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGATCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTAAACGCTTTGTGCCGATC > NZ_CP009273/1153616‑1153789
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ 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
GGTTGCGCCACTGGTACTGCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGATCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTAAACGCTTTGTGCCGATCATTTCTGGCC > NZ_CP009273/1153609‑1153799
|
GGTTGCGCCACTGGTACTGCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCA > SRR3722079.42624/1‑100 (MQ=60)
CCACTGGTACTGCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGATCGCAGCGTACA < SRR3722079.244278/100‑1 (MQ=60)
TGCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCG < SRR3722079.344192/100‑1 (MQ=60)
GCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGT > SRR3722079.139385/1‑100 (MQ=60)
CCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGA > SRR3722079.363690/1‑100 (MQ=60)
GGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTC > SRR3722079.291108/1‑100 (MQ=60)
GGGATTATCTCCGGTGCGATCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTAAACGCTTTGTGC < SRR3722079.431897/100‑1 (MQ=60)
TATCTCCGGTGCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTAAACGCTTTGTGCCGATC < SRR3722079.629183/100‑1 (MQ=60)
GCGTTCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTAAACGCTTTGTGCCGATCATTTCTGGCC < SRR3722079.717144/100‑1 (MQ=60)
|
GGTTGCGCCACTGGTACTGCATTTACCTGCTGAAGAAATCGCCTCTAAACACCTGGCGGATACTGGCGTACTCGGAGGGATTATCTCCGGTGCGATCGCAGCGTACATGTTTAACCGTTTCTACCGTATTAAGCTGCCTGAGTATCTTGGCTTCTTTGCCGGTAAACGCTTTGTGCCGATCATTTCTGGCC > NZ_CP009273/1153609‑1153799
|
| 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: ‑ |
