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 |
4,087,693 |
T→C |
F10F (TTT→TTC) |
rhaS → |
HTH‑type transcriptional activator RhaS |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,087,693 | 0 | T | C | 100.0%
| 43.8
/ NA
| 14 | F10F (TTT→TTC) | rhaS | HTH‑type transcriptional activator RhaS |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (10/4); total (10/4) |
TAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTTCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTCAT > NZ_CP009273/4087607‑4087771
|
caaGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCg < 1:25508/89‑1 (MQ=255)
tACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGc < 2:159738/90‑1 (MQ=255)
aTTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATa > 1:260007/1‑90 (MQ=255)
gCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAAcc > 2:28579/1‑90 (MQ=255)
gaggCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGAt < 1:217136/90‑1 (MQ=255)
gCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGAtttt > 1:46543/1‑90 (MQ=255)
cGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAAcatca > 2:239946/1‑90 (MQ=255)
gTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGAt < 1:26017/75‑1 (MQ=255)
gTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGAt > 2:26017/1‑75 (MQ=255)
aTTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAAcatcatca > 2:204560/1‑90 (MQ=255)
tAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCTTGAACATCATCATGAttt > 1:19654/1‑90 (MQ=255)
gtgtGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTc > 1:58094/1‑90 (MQ=255)
gtgtGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTc > 1:60683/1‑90 (MQ=255)
gtgGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTCAt > 2:286006/1‑90 (MQ=255)
|
TAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTTCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTCAT > NZ_CP009273/4087607‑4087771
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ 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
TAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTTCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTC > NZ_CP009273/4087607‑4087769
|
CAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACG < SRR3722116.25839/100‑1 (MQ=60)
CGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATA > SRR3722116.263716/1‑100 (MQ=60)
ACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTT > SRR3722116.47113/1‑100 (MQ=60)
gacagCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAAC < SRR3722116.26353/95‑1 (MQ=60)
GAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAAC < SRR3722116.219966/100‑1 (MQ=60)
CCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCTTGAACATCATCATGATTT > SRR3722116.19918/1‑100 (MQ=60)
GTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTC > SRR3722116.58802/1‑100 (MQ=60)
GTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTC > SRR3722116.61424/1‑100 (MQ=60)
|
TAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTTCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTC > NZ_CP009273/4087607‑4087769
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
