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 |
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%
| 57.9
/ NA
| 19 | H143H (CAT→CAC) | rraA | ribonuclease E activity regulator RraA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (13/6); total (13/6) |
AAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGATGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCA > NZ_CP009273/4108744‑4108905
|
aaaaaaGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTgg < 1:107088/90‑1 (MQ=255)
tttCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGacac > 1:33267/1‑90 (MQ=255)
ttCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACAcc > 1:207268/1‑90 (MQ=255)
ttCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGGATTGTCGGCATAAAGGGGGTCGCCGGAGAAGAAGGTGACAcc > 1:76417/1‑90 (MQ=255)
tATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGCCGCCGGAGAAGAAGGGGACACCGCCa > 2:485225/1‑90 (MQ=255)
cAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGAc > 2:49675/1‑90 (MQ=255)
cAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGAc > 1:334803/1‑90 (MQ=255)
aGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACa > 2:75035/1‑90 (MQ=255)
gCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACAt < 1:125475/90‑1 (MQ=255)
gATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGc > 2:259841/1‑90 (MQ=255)
tctGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCg > 1:226745/1‑90 (MQ=255)
aaaGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCaa < 2:248975/90‑1 (MQ=255)
aaaGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCaa < 2:39724/90‑1 (MQ=255)
ataatCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCt > 1:242961/1‑90 (MQ=255)
taatCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCtt > 1:23051/1‑90 (MQ=255)
ggTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGc > 1:237631/1‑90 (MQ=255)
ttGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCa < 1:236395/90‑1 (MQ=255)
cATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCtt < 1:254931/59‑1 (MQ=255)
cATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCtt > 2:254931/1‑59 (MQ=255)
|
AAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGATGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCA > NZ_CP009273/4108744‑4108905
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ 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
ACAGGTAACGCAGAAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGATGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCGGAATTGCCG > NZ_CP009273/4108731‑4108921
|
ACAGGTAACGCAGAAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGG < SRR3722094.345412/100‑1 (MQ=60)
ACAGGTAACGCAGAAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGG < SRR3722094.478030/100‑1 (MQ=60)
AAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGA < SRR3722094.108631/100‑1 (MQ=60)
TTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACAC > SRR3722094.33737/1‑100 (MQ=60)
TGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACC > SRR3722094.210069/1‑100 (MQ=60)
TGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGGATTGTCGGCATAAAGGGGGTCGCCGGAGAAGAAGGTGACACC > SRR3722094.77510/1‑100 (MQ=60)
ATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGAC > SRR3722094.340295/1‑100 (MQ=60)
CAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCG > SRR3722094.229823/1‑100 (MQ=60)
GCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCC < SRR3722094.127281/100‑1 (MQ=60)
tcagatgtgtataagagacaGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGC < SRR3722094.258682/80‑1 (MQ=60)
TTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCT > SRR3722094.246458/1‑100 (MQ=60)
TCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTT > SRR3722094.23387/1‑100 (MQ=60)
GAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGC > SRR3722094.241006/1‑100 (MQ=60)
TTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCGGAA < SRR3722094.239741/100‑1 (MQ=60)
GCACAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCGGAATTGCCG > SRR3722094.218640/1‑100 (MQ=60)
|
ACAGGTAACGCAGAAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGATGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCGGAATTGCCG > NZ_CP009273/4108731‑4108921
|
| 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: ‑ |
