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 I211 R1
|
223 |
18.0 |
1007644 |
96.3% |
970361 |
85.7 |
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%
| 72.9
/ NA
| 18 | coding (513/960 nt) | nrdF | class 1b ribonucleoside‑diphosphate reductase subunit beta |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (3/15); total (3/15) |
GGTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATA > NZ_CP009273/2797290‑2797457
|
ggTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTAttttcca > 2:332664/1‑87 (MQ=255)
tgatgaTCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGc < 1:359981/90‑1 (MQ=255)
atCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCgg < 2:243987/90‑1 (MQ=255)
cGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGaaa < 2:443458/90‑1 (MQ=255)
gCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAg > 1:98166/1‑90 (MQ=255)
gCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAg > 2:60800/1‑90 (MQ=255)
cTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGc < 1:332664/90‑1 (MQ=255)
gAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAAt < 2:39386/90‑1 (MQ=255)
tCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACcgc < 2:203719/90‑1 (MQ=255)
gtTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATc < 1:92699/90‑1 (MQ=255)
aTTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGc < 2:455456/90‑1 (MQ=255)
ggTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTcc > 1:106324/1‑90 (MQ=255)
ggTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTcc < 1:490583/90‑1 (MQ=255)
tttCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCAc < 2:98166/90‑1 (MQ=255)
tttCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCAc < 2:6539/90‑1 (MQ=255)
ttCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACg < 2:106956/90‑1 (MQ=255)
tGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGtt < 1:152169/90‑1 (MQ=255)
tGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGtt < 1:144948/90‑1 (MQ=255)
gATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATa < 2:55206/90‑1 (MQ=255)
|
GGTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATA > NZ_CP009273/2797290‑2797457
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ 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
GTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGGCTATAA > NZ_CP009273/2797291‑2797465
|
GTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAG > SRR3722094.99587/1‑100 (MQ=60)
TGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGC < SRR3722094.366012/100‑1 (MQ=60)
CTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATAC < SRR3722094.338106/100‑1 (MQ=60)
GTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTA < SRR3722094.94046/100‑1 (MQ=60)
GTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCC > SRR3722094.107852/1‑100 (MQ=60)
GGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTA < SRR3722094.499231/100‑1 (MQ=60)
TGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGG < SRR3722094.146982/100‑1 (MQ=60)
TGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGG < SRR3722094.154291/100‑1 (MQ=60)
CCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGGCTATAA > SRR3722094.113270/1‑100 (MQ=60)
|
GTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGGCTATAA > NZ_CP009273/2797291‑2797465
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
