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 I208 R1
|
222 |
13.1 |
731276 |
96.6% |
706412 |
85.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,492,074 |
(T)5→4 |
intergenic (‑300/‑76) |
alaC ← / → ypdA |
alanine transaminase/two‑component system sensor histidine kinase YpdA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,492,070 | 0 | T | . | 100.0%
| 34.7
/ NA
| 9 | intergenic (‑296/‑80) | alaC/ypdA | alanine transaminase/two‑component system sensor histidine kinase YpdA |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (4/5); total (4/5) |
TGCATTATCAAGAGATGCATTGCTAATACACCATTTATCTATCAATCCCCTTTTAAAATTGTGGTTTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCTTCAGGTTACCTATCATAGAGGTTTAATCCTTATTCAGAGTCACCCGTG > NZ_CP009273/2492006‑2492152
|
tGCATTATCAAGAGATGCATTGCTAATACACCATTTATCTATCAATCCCCTTTTAAAATTGTGG‑TTTTCATCAAAAACGGCCTGCTGGtc < 2:283288/90‑1 (MQ=255)
tATCAAGAGATGCATTGCTAATACACCATTTATCTATCAATCCCCTTTTAAAATTGTGG‑TTTTCCTCAAAAACGGCCTGCTGGTCATCAg > 2:138085/1‑90 (MQ=255)
aaGAGATGCATTGCTAATACACCATTTATCTATCAATCCCCTTTTAAAATTGTGG‑TTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCtt > 1:232342/1‑90 (MQ=255)
aTGCATTGCTAATACACCATTTATCTATCAATCCCCTTTTAAAATTGTGG‑TTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCTTCAGGt < 2:184429/90‑1 (MQ=255)
aTTGCTAATACACCATTTATCTATCAATCCCCTTTTAAAATTGTGG‑TTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCTTCAGGTTAcc < 2:232342/90‑1 (MQ=255)
atcAATCCCCTTTTAAAATTGTGG‑TTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCTTCAGGTTACCTATCATAGAGGTTTAATCCTTa > 1:48390/1‑90 (MQ=255)
ttttAAAATTGTGG‑TTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCTTCAGGTTACCTATCATAGAGGTTTAAt > 1:200951/1‑75 (MQ=255)
ttttAAAATTGTGG‑TTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCTTCAGGTTACCTATCATAGAGGTTTAAt < 2:200951/75‑1 (MQ=255)
aaTTGTGG‑TTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCTTCAGGTTACCTATCATAGAGGTTTAATCCTTATTCAGAGTCACCCGTg < 1:210088/90‑1 (MQ=255)
|
TGCATTATCAAGAGATGCATTGCTAATACACCATTTATCTATCAATCCCCTTTTAAAATTGTGGTTTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCTTCAGGTTACCTATCATAGAGGTTTAATCCTTATTCAGAGTCACCCGTG > NZ_CP009273/2492006‑2492152
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GTGCATTATCAAGAGATGCATTGCTAATACACCATTTATCTATCAATCCCCTTTTAAAATTGTGGTTTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCTTCAGGTTACCTATCATAGAGGTTTAATCCTTATTCAGAGTCACCCGTGCACGAAATAT > NZ_CP009273/2492005‑2492162
|
GTGCATTATCAAGAGATGCATTGCTAATACACCATTTATCTATCAATCCCCTTTTAAAATTGTGG‑TTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCTT > SRR3722090.235049/1‑100 (MQ=60)
CCATTTATCTATCAATCCCCTTTTAAAATTGTGG‑TTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCTTCAGGTTACCTATCATAGAGGTTTAATCCTTA > SRR3722090.48904/1‑100 (MQ=60)
ATCAATCCCCTTTTAAAATTGTGG‑TTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCTTCAGGTTACCTATCATAGAGGTTTAATCCTTATTCAGctgtc > SRR3722090.203175/1‑95 (MQ=60)
AATTGTGG‑TTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCTTCAGGTTACCTATCATAGAGGTTTAATCCTTATTCAGAGTCACCCGTGCACGAAATAT < SRR3722090.212424/100‑1 (MQ=60)
|
GTGCATTATCAAGAGATGCATTGCTAATACACCATTTATCTATCAATCCCCTTTTAAAATTGTGGTTTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCTTCAGGTTACCTATCATAGAGGTTTAATCCTTATTCAGAGTCACCCGTGCACGAAATAT > NZ_CP009273/2492005‑2492162
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
