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 I205 R1
|
220 |
17.5 |
961422 |
97.1% |
933540 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,108,830 |
A→G |
H143H (CAT→CAC) |
rraA ← |
ribonuclease E activity regulator RraA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,108,830 | 0 | A | G | 100.0%
| 59.1
/ NA
| 18 | H143H (CAT→CAC) | rraA | ribonuclease E activity regulator RraA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (15/3); total (15/3) |
CACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGATGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCG > NZ_CP009273/4108752‑4108912
|
cACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGga < 1:263222/90‑1 (MQ=255)
aCCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGgag > 2:480676/1‑90 (MQ=255)
tttCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGacac > 1:283256/1‑90 (MQ=255)
tATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCa > 2:264914/1‑90 (MQ=255)
ttCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGagaag > 2:109191/1‑70 (MQ=255)
ttCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGagaag < 1:109191/70‑1 (MQ=255)
ttCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAAtt > 2:419894/1‑90 (MQ=255)
cAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGAc > 2:350997/1‑90 (MQ=255)
aGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACa > 2:430168/1‑90 (MQ=255)
gATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGagaag > 1:345505/1‑56 (MQ=255)
gATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGagaag < 2:345505/56‑1 (MQ=255)
gATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGc > 1:376622/1‑90 (MQ=255)
tcttctGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCtt > 2:306707/1‑90 (MQ=255)
ttctGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCtctc > 2:378022/1‑90 (MQ=255)
ctGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGc > 2:205932/1‑90 (MQ=255)
gTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCAcc > 1:5845/1‑90 (MQ=255)
gTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCAcc > 1:155927/1‑90 (MQ=255)
cATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCg > 1:249706/1‑90 (MQ=255)
|
CACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGATGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCG > NZ_CP009273/4108752‑4108912
|
| 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
CACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGATGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCG > NZ_CP009273/4108752‑4108912
|
CACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTG < SRR3722087.265802/100‑1 (MQ=60)
taagagacagTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACAC < SRR3722087.110244/90‑1 (MQ=60)
TTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACAC > SRR3722087.286087/1‑100 (MQ=60)
ATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCtgtctcttatacacatctccgag > SRR3722087.349371/1‑77 (MQ=60)
ATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGC > SRR3722087.380947/1‑100 (MQ=60)
TCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACC > SRR3722087.157362/1‑100 (MQ=60)
TCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACC > SRR3722087.5898/1‑100 (MQ=60)
GTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCG > SRR3722087.252123/1‑100 (MQ=60)
|
CACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGATGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCG > NZ_CP009273/4108752‑4108912
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
