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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,797,377 |
(T)5→4 |
coding (517/960 nt) |
nrdF → |
class 1b ribonucleoside‑diphosphate reductase subunit beta |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,797,373 | 0 | T | . | 94.1%
| 58.0
/ ‑0.9
| 17 | coding (513/960 nt) | nrdF | class 1b ribonucleoside‑diphosphate reductase subunit beta |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base . (5/11); total (5/12) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.97e-01 |
ATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTAC > NZ_CP009273/2797297‑2797451
|
atCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCgg < 1:173838/90‑1 (MQ=255)
cTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGc < 1:283432/90‑1 (MQ=255)
cTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGc < 2:301031/90‑1 (MQ=255)
ccAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCgg < 2:156794/90‑1 (MQ=255)
tttCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATcc > 1:387927/1‑90 (MQ=255)
tGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCgg < 1:576865/76‑1 (MQ=255)
tGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCgg > 2:576865/1‑76 (MQ=255)
tGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTg > 1:73815/1‑90 (MQ=255)
tCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTa > 2:298669/1‑90 (MQ=255)
gTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCa < 2:155779/90‑1 (MQ=255)
tttCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCAc < 2:518082/90‑1 (MQ=255)
ttCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACg < 1:298669/90‑1 (MQ=255)
ttCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACg < 2:335941/90‑1 (MQ=255)
ttCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACg < 2:541759/90‑1 (MQ=255)
cTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGt > 1:274052/1‑90 (MQ=255)
tGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGtt < 2:57820/90‑1 (MQ=255)
gCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTtac < 2:375639/90‑1 (MQ=255)
|
ATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTAC > NZ_CP009273/2797297‑2797451
|
| 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
ATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGGCTATAAATATC > NZ_CP009273/2797297‑2797470
|
ATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACC < SRR3722111.176005/100‑1 (MQ=60)
CTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATAC < SRR3722111.287009/100‑1 (MQ=60)
CGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCC > SRR3722111.393530/1‑100 (MQ=60)
acagGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCG < SRR3722111.585918/96‑1 (MQ=60)
GTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTG > SRR3722111.74704/1‑100 (MQ=60)
cgtcggcagcgtcagatgtgtataagagacaggtaTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGC < SRR3722111.278204/65‑1 (MQ=60)
ATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGT > SRR3722111.277434/1‑100 (MQ=60)
TTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACAT < SRR3722111.302516/100‑1 (MQ=60)
GTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGGCTATAAATATC > SRR3722111.561510/1‑100 (MQ=60)
|
ATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGGCTATAAATATC > NZ_CP009273/2797297‑2797470
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
