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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
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 | 88.0%
| 69.1
/ 3.5
| 25 | W242C (TGG→TGC) | yehP | VWA domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base G (1/2); new base C (11/11); total (12/13) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.89e-01 |
TTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAGAGT > NZ_CP009273/2202100‑2202256
|
ttACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCTCTCTGCGGTGATGGTGGCCTGTTTGTGCCAGTTACCCGGCATTctt < 2:809136/90‑3 (MQ=255)
cTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTAcc < 1:355585/90‑1 (MQ=255)
cTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTAcc < 1:708120/90‑1 (MQ=255)
ttGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATc > 1:370361/1‑90 (MQ=255)
gATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTg > 1:291282/1‑90 (MQ=255)
cGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTa > 1:712448/1‑62 (MQ=255)
cGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTa < 2:712448/62‑1 (MQ=255)
aTTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGcgtcg > 1:42656/1‑90 (MQ=255)
cGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTg < 2:372562/90‑1 (MQ=255)
aTCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGAtctc < 1:259610/90‑1 (MQ=255)
ccACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTAcc > 2:751799/1‑52 (MQ=255)
ccACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTAcc < 1:751799/52‑1 (MQ=255)
aCTCTGCGGTGATGGCGGCCTGTTTGGGCCAGTTACCCGGCATTCGTACCCATCTGGGGGCGTTAGACACAAGCGTAGCTGGTTTCACgt > 2:841129/1‑89 (MQ=255)
ctctGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGc < 2:575678/90‑1 (MQ=255)
tctGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCa < 2:42656/90‑1 (MQ=255)
gCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGAc > 2:353492/1‑90 (MQ=255)
gCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGAc > 1:772309/1‑90 (MQ=255)
gATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGc > 2:456437/1‑90 (MQ=255)
aTGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGcc < 1:496498/90‑1 (MQ=255)
ggcggcCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGa > 2:56933/1‑90 (MQ=255)
gcggcCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGAt < 2:133706/90‑1 (MQ=255)
cggcCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGGGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATc > 2:413792/1‑90 (MQ=255)
ccTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCgg > 1:402182/1‑90 (MQ=255)
gTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTag < 2:402182/90‑1 (MQ=255)
tgtgCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAGAGt < 1:456437/90‑1 (MQ=255)
|
TTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAGAGT > NZ_CP009273/2202100‑2202256
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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
GTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAGAGTTATTAATGAA > NZ_CP009273/2202097‑2202266
|
GTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATC > SRR3722079.373330/1‑100 (MQ=60)
tgggctcggagatgtgtataagagacaGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGG < SRR3722079.759834/73‑1 (MQ=60)
CTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGG < SRR3722079.358373/100‑1 (MQ=60)
CTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGG < SRR3722079.715640/100‑1 (MQ=60)
GATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTG > SRR3722079.293682/1‑100 (MQ=60)
GATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTctgtctcttatacacatc > SRR3722079.720028/1‑82 (MQ=60)
TCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCG > SRR3722079.42979/1‑100 (MQ=60)
GATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGAC > SRR3722079.780577/1‑100 (MQ=60)
ATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACG < SRR3722079.261790/100‑1 (MQ=60)
GTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGG > SRR3722079.405583/1‑100 (MQ=60)
ATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAG < SRR3722079.500913/100‑1 (MQ=60)
TGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAGAGTTATTAATGAA < SRR3722079.460434/100‑1 (MQ=60)
|
GTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAGAGTTATTAATGAA > NZ_CP009273/2202097‑2202266
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
