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 |
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 | . | 100.0%
| 47.2
/ NA
| 12 | coding (513/960 nt) | nrdF | class 1b ribonucleoside‑diphosphate reductase subunit beta |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (3/9); total (3/9) |
CGCGGTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACAT > NZ_CP009273/2797287‑2797456
|
cgcgGTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTAtttt > 1:261594/1‑90 (MQ=255)
ggTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTAttttcca > 1:90297/1‑87 (MQ=255)
cTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGc < 1:70832/90‑1 (MQ=255)
gAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTg < 2:261594/90‑1 (MQ=255)
aGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCaa > 2:325503/1‑90 (MQ=255)
aaTCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGAt > 2:124710/1‑90 (MQ=255)
gTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGAt < 2:45404/90‑1 (MQ=255)
aTTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGc < 2:134060/90‑1 (MQ=255)
ggTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTcc > 1:85133/1‑90 (MQ=255)
ggTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTcc < 2:256326/90‑1 (MQ=255)
tttCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCAc < 2:135661/90‑1 (MQ=255)
ggCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTta < 2:90297/90‑1 (MQ=255)
cGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACAt < 1:124710/90‑1 (MQ=255)
cGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACAt < 1:351509/90‑1 (MQ=255)
|
CGCGGTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACAT > NZ_CP009273/2797287‑2797456
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ACATTATCGCGGTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGGCTATAAATATC > NZ_CP009273/2797280‑2797470
|
ACATTATCGCGGTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCA > SRR3722116.91415/1‑100 (MQ=60)
CTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATAC < SRR3722116.71717/100‑1 (MQ=60)
GTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCC > SRR3722116.86188/1‑100 (MQ=60)
CGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGGCTATAAA < SRR3722116.126199/100‑1 (MQ=60)
CGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGGCTATAAA < SRR3722116.356735/100‑1 (MQ=60)
GTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACtgtctcttatacacat > SRR3722116.38527/1‑84 (MQ=60)
|
ACATTATCGCGGTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGGCTATAAATATC > NZ_CP009273/2797280‑2797470
|
| 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: ‑ |
