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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,798,416 |
(T)8→7 |
coding (61/936 nt) |
rfaS ← |
LPS core biosynthesis protein RfaS |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,798,409 | 0 | T | . | 100.0%
| 67.8
/ NA
| 17 | coding (68/936 nt) | rfaS | LPS core biosynthesis protein RfaS |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (11/6); total (11/6) |
TCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAG > NZ_CP009273/3798338‑3798493
|
tccCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAAt > 2:173195/1‑90 (MQ=255)
tccCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAAt > 2:1468265/1‑90 (MQ=255)
tccCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAAt > 1:321192/1‑90 (MQ=255)
tccCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAAt > 2:1001628/1‑90 (MQ=255)
tccCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TCTTTTTCAGGTACTGAAt > 2:1153043/1‑90 (MQ=255)
aTCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAAccc < 2:1337310/90‑1 (MQ=255)
atatTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTtata < 1:1001628/90‑1 (MQ=255)
tatTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTataa > 1:1331259/1‑90 (MQ=255)
tttttGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTataaaata > 1:284381/1‑90 (MQ=255)
atatTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCAtaataa < 1:1185887/90‑1 (MQ=255)
tttttATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAagtt > 2:734753/1‑90 (MQ=255)
ttttATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAagtta < 1:1546463/90‑1 (MQ=255)
ttATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAagttagt > 2:493723/1‑90 (MQ=255)
aTCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTc < 1:959551/90‑1 (MQ=255)
tCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTcc > 2:1051195/1‑90 (MQ=255)
tCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTcc < 2:1331259/90‑1 (MQ=255)
ttGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAg > 1:318767/1‑90 (MQ=255)
|
TCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAG > NZ_CP009273/3798338‑3798493
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ 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
GCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAGTACATACTAATAAAT > NZ_CP009273/3798328‑3798508
|
GCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAAT > SRR3722078.325121/1‑100 (MQ=60)
AATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAA > SRR3722078.1352574/1‑100 (MQ=60)
CAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATA > SRR3722078.287851/1‑100 (MQ=60)
ATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAG < SRR3722078.1016272/100‑1 (MQ=60)
ATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCC < SRR3722078.1204427/100‑1 (MQ=60)
ATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAG > SRR3722078.322673/1‑100 (MQ=60)
TTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAGTAC < SRR3722078.1571659/100‑1 (MQ=60)
ATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAGTACATAC < SRR3722078.973155/100‑1 (MQ=60)
CTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAGTACATACTAATAAAT < SRR3722078.190490/100‑1 (MQ=60)
|
GCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAGTACATACTAATAAAT > NZ_CP009273/3798328‑3798508
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
