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 |
|
A4 F28 I1 R1
|
128 |
54.7 |
1845674 |
99.3% |
1832754 |
139.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,947,713 |
(T)7→8 |
intergenic (+30/+44) |
metV → / ← amiC |
tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase C |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,947,706 | 1 | . | T | 92.9%
| 84.4
/ ‑0.0
| 28 | intergenic (+23/+51) | metV/amiC | tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase C |
| Reads supporting (aligned to +/- strand): ref base . (2/0); new base T (15/11); total (17/11) |
| Fisher's exact test for biased strand distribution p-value = 5.05e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01 |
TACGGTGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTG‑‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAGCGCCTTTTTATCATCCCCTTCTCGCCAGCGTCGCCCCATCGGCAAAATACGCTTTAATCCCCGCAAGAATAGACTCCGCAACTTCCTGCTG > NC_000913/2947599‑2947837
|
tACGGTGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAgc > 1:249564/1‑140 (MQ=255)
aCGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTGTACACCCA‑AAAGGGGGA‑TTTTTTTGATTCTGGGCTCCCA‑TAAAAAAGAGCCCTTc > 2:599302/1‑140 (MQ=17)
aCGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTc > 2:517517/1‑140 (MQ=255)
gcgGGGTGGAGCAGTCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAg < 2:905115/140‑1 (MQ=255)
cgGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAgc > 1:654956/1‑140 (MQ=255)
cgGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTG‑‑TTTTTTTGTTTTTTGTCTTCCATTAAAAAAGCCCCAtcaacc > 1:316395/1‑135 (MQ=18)
ggggTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAgcg < 1:599302/140‑1 (MQ=255)
gAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTG‑‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAGCGCCttttt > 2:728251/1‑140 (MQ=255)
gcagcCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAGCGCCTTTTTa < 1:791803/140‑1 (MQ=255)
ccTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAgc > 2:817734/1‑127 (MQ=255)
ccTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAgc < 1:817734/127‑1 (MQ=255)
aGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAGCGCCTTTTTATCATCCCCtt < 1:379569/140‑1 (MQ=255)
cgtcgGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTGATCACCCT‑AACGGGGGA‑TTATTTTGATTCGGGTCGCCCC‑TAAAAAAGAGCCATTCAGCCCCTTATTATCATCCCCTtctgt > 2:341871/1‑138 (MQ=21)
cgtcgGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTGTTTTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAGCGCCTTTTTATCATCCCCTtctc > 2:605053/1‑140 (MQ=255)
cgtcgGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAGCGCCTTTTTATCATCCCCTTCTCg > 2:204414/1‑140 (MQ=255)
tcgGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTTTACACGCTGAAGGGGGA‑‑TTTTTTTGATGCTGGGCGCCCA‑TAAAAGAGCGCCATTCAGCCCCATTTTATCATCCCCTTCTCGcc > 2:379569/1‑140 (MQ=18)
cccGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAGCGCCTTTTTATCATCCCCTTCTCGCCAGCGTCGCCCCa < 2:654956/140‑1 (MQ=255)
aaGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAGCGCCTTTTTATCATCCCCTTCTCGCCAGCGTCGCCCCATCgg > 1:909146/1‑140 (MQ=255)
aaGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAGCGCCTTTTTATCATCCCCTTCTCGCCAGCGTCGCCCCATCgg > 1:261597/1‑140 (MQ=255)
aaGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAGCGCCTTTTTATCATCCCCTTCTCGCCAGCGTCGCCCCATCgg > 1:358888/1‑140 (MQ=255)
ggTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAGCGCCTTTTTATCATCCCCTTCTCGCCAGCGTCGCCCCATCGGCa < 2:249564/140‑1 (MQ=255)
ggTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAGCGCCTTTTTATCATCCCCTTCTCGCCAGCGTCGCCCCATCGGCa > 2:595032/1‑140 (MQ=255)
gtcgGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAGCGCCTTTTTATCATCCCCTTCTCGCCAGCGTCGCCCCATCGGCAAAAt < 1:341871/140‑1 (MQ=255)
tcgGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAGCGCCTTTTTATCATCCCCTTCTCGCCAGCGTCGCCCCATCGGCAAAATa > 1:566909/1‑140 (MQ=255)
tcgGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAGCGCCTTTTTATCATCCCCTTCTCGCCAGCGTCGCCCCATCGGCAAAATa > 1:519227/1‑140 (MQ=255)
gCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAGCGCCTTTTTATCATCCCCTTCTCGCCAGCGTCGCCCCATCGGCAAAATACGCTTTAATCCCCg < 2:358888/140‑1 (MQ=255)
gCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAGCGCCTTTTTATCATCCCCTTCTCGCCAGCGTCGCCCCATCGGCAAAATACGCTTTAATCCCCg > 1:618053/1‑140 (MQ=255)
ccAATTATTGAACACCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAGCGCCTTTTTATCATCCCCTTCTCGCCAGCGTCGCCCCATCGGCAAAATACGCTTTAATCCCCGCAAGAATAGa < 1:595032/140‑1 (MQ=255)
cacCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAGCGCCTTTTTATCATCCCCTTCTCGCCAGCGTCGCCCCATCGGCAAAATACGCTTTAATCCCCGCAAGAATAGACTCCGCAACTTc > 2:575216/1‑140 (MQ=255)
acCCT‑AACGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAGCGCCTTTTTATCATCCCCTTCTCGCCAGCGTCGCCCCATCGGCAAAATACGCTTTAATCCCCGCAAGAATAGACTCCGCAACTTcc < 2:566909/140‑1 (MQ=255)
aaCGGGTGT‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAGCGCCTTTTTATCACCCCCTTCTCGCCAGCGTCGCCCCATCGGCAAAATACGCTTTAATCCCCGCAAGAATAGACTCCGCAACTTCctgctg > 1:121146/1‑140 (MQ=255)
|
TACGGTGACGCGGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTCGGTTCAAATCCGGCCCCCGCAACCAATTATTGAACACCCT‑AACGGGTG‑‑TTTTTTTGTTTCTGGTCTCCCA‑TAAAAAAGCGCCATTCAGCGCCTTTTTATCATCCCCTTCTCGCCAGCGTCGCCCCATCGGCAAAATACGCTTTAATCCCCGCAAGAATAGACTCCGCAACTTCCTGCTG > NC_000913/2947599‑2947837
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
