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 |
2,202,171 |
G→C |
W242C (TGG→TGC) |
yehP → |
VWA domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,202,171 | 0 | G | C | 100.0%
| 70.5
/ NA
| 22 | W242C (TGG→TGC) | yehP | VWA domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (11/11); total (11/11) |
CTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAG > NZ_CP009273/2202094‑2202253
|
cTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGc < 2:323598/90‑1 (MQ=255)
tACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTa > 1:337236/1‑90 (MQ=255)
tGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTAccc > 2:276323/1‑90 (MQ=255)
gTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCAt > 1:346901/1‑90 (MQ=255)
ttGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATc < 2:388653/90‑1 (MQ=255)
ttGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGGGCCAGTTACCCGGCCTTCGTACCCATc > 1:471555/1‑90 (MQ=255)
tGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCt > 2:159120/1‑90 (MQ=255)
gATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGacac < 2:475217/90‑1 (MQ=255)
gTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGc < 2:117444/90‑1 (MQ=255)
gTCGATTCGGTGATCCACTCTGCGATGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGc < 2:336783/90‑1 (MQ=255)
cGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTg < 1:39378/90‑1 (MQ=255)
gTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGAt > 2:122222/1‑90 (MQ=255)
aTCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGAtctc < 2:467767/90‑1 (MQ=255)
ccACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCAc > 2:58874/1‑90 (MQ=255)
ctGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAg > 1:246453/1‑90 (MQ=255)
gCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGAc < 2:31150/90‑1 (MQ=255)
gCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGAc > 2:273636/1‑90 (MQ=255)
gCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGAc < 1:28829/90‑1 (MQ=255)
gcggcCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGAt < 2:346901/90‑1 (MQ=255)
cggcCTGTTTGTGCCAGTTACCCGGCATTCGTACCCCTCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATc > 1:248533/1‑90 (MQ=255)
cggcCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATc > 1:164610/1‑90 (MQ=255)
gTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTag < 2:28305/90‑1 (MQ=255)
|
CTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAG > NZ_CP009273/2202094‑2202253
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 30 ≤ 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
CGCCAAAGCGAACAATGGCAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATC > NZ_CP009273/2202073‑2202247
|
CGCCAAAGCGAACAATGGCAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCC > SRR3722094.119142/1‑100 (MQ=60)
CAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTA > SRR3722094.342774/1‑100 (MQ=60)
GGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCAT > SRR3722094.352653/1‑100 (MQ=60)
GTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGGGCCAGTTACCCGGCCTTCGTACCCATC > SRR3722094.479887/1‑100 (MQ=60)
CGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGC < SRR3722094.39935/100‑1 (MQ=60)
GTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAG > SRR3722094.250019/1‑100 (MQ=60)
GCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCCTCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATC > SRR3722094.252141/1‑100 (MQ=60)
GCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATC > SRR3722094.166908/1‑100 (MQ=60)
GCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATC < SRR3722094.29253/100‑1 (MQ=60)
|
CGCCAAAGCGAACAATGGCAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATC > NZ_CP009273/2202073‑2202247
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
