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 F3 I122 R1
|
193 |
20.9 |
1228102 |
94.7% |
1163012 |
84.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,662,649 |
T→G |
H58P (CAC→CCC) |
mlc ← |
DNA‑binding transcriptional repressor Mlc |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,662,649 | 0 | T | G | 100.0%
| 51.3
/ NA
| 15 | H58P (CAC→CCC) | mlc | DNA‑binding transcriptional repressor Mlc |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (8/7); total (8/7) |
GTGCCAGGCTTCAGTTTCAACCACCAGCCCCACCGCCGGACGGCCACGGTTCCCCGCTTCTTTGATTTCCAGCTCTTGCACCAGGTGTGCTTCGAGCATCTCACGGACAATTTTAGTGATACTGGCAGGAGCCAGTTGCGCCAGACGGGAAAGATCGATACGC > NZ_CP009273/1662564‑1662726
|
gTGCCAGGCTTCAGTTTCAACCACCAGCCCCACCGCCGGACGGCCACGGTTCCCCGCTTCTTTGATTTCCAGCTCTTGCACCAGGGGTGc > 2:357740/1‑90 (MQ=255)
gTGCCAGGCTTCAGTTTCAACCACCAGCCCCACCGCCGGACGGCCACGGTTCCCCGCTTCTTTGATTTCCAGCTCTTGCACCAGGGGTGc > 2:408898/1‑90 (MQ=255)
gCCAGGCTTCAGTTTCAACCACCAGCCCCACCGCCGGACGGCCACGGTTCCCCGCTTCTTTGATTTCCAGCTCTTGCACCAGGGGTGCtt > 2:574406/1‑90 (MQ=255)
ggCTTCAGTTTCAACCACCAGCCCCACCGCCGGACGGCCACGGTTCCCCGCTTCTTTGATTTCCAGCTCTTGCACCAGGGGTGCTTCGAg > 2:481115/1‑90 (MQ=255)
cTTCAGTTTCAACCACCAGCCCCACCGCCGGACGGCCACGGTTCCCCGCTTCTTTGATTTCCAGCTCTTGCACCAGGGGTGCTTCGAGCa < 2:166162/90‑1 (MQ=255)
aaCCACCAGCCCCACCGCCGGACGGCCACGGTTCCCCGCTTCTTTGATTTCCAGCTCTTGCACCAGGGGTGCTTCGAGCATCTCACGGAc < 1:408898/90‑1 (MQ=255)
aGCCCCACCGCCGGACGGCCACGGTTCCCCGCTTCTTTGATTTCCAGCTCTTGCACCAGGGGTGCTTCGAGCATCTCACGGACAAttt < 1:362858/88‑1 (MQ=255)
aGCCCCACCGCCGGACGGCCACGGTTCCCCGCTTCTTTGATTTCCAGCTCTTGCACCAGGGGTGCTTCGAGCATCTCACGGACAAttt > 2:362858/1‑88 (MQ=255)
cACCGCCGGACGGCCACGGTTCCCCGCTTCTTTGATTTCCAGCTCTTGCACCAGGGGTGCTTCGAGCATCTCACGGACAATTTTAGTGAt > 1:391258/1‑90 (MQ=255)
gCCACGGTTCCCCGCTTCTTTGATTTCCAGCTCTTGCACCAGGGGTGCTTCGAGCATCTCACGGACAATTTTAGTGATACTGGCAGGAGc > 2:58027/1‑90 (MQ=255)
ccccGCTTCTTTGATTTCCAGCTCTTGCACCAGGGGTGCTTCGAGCATCTCACGGACAATTTTAGTGATACTGGCAGGAGCCAGTTgcgc < 2:43130/90‑1 (MQ=255)
tttCCAGCTCTTGCACCAGGGGTGCTTCGAGCATCTCACGGACAATTTTAGTGATACTGGCAGGGGCCAGTTGCGCCAGACGGGAAAGAt > 1:570438/1‑90 (MQ=255)
ccAGCTCTTGCACCAGGGGTGCTTCGAGCATCTCACGGACAATTTTAGTGATACTGGCAGGAGCCAGTTGCGCCAGACGGGAAAGATCGa < 2:382310/90‑1 (MQ=255)
tctTGCACCAGGGGTGCTTCGAGCATCTCACGGACAATTTTAGTGATACTGGCAGGAGCCAGTTGCGCCAGACGGGAAAGATCGATAcgc < 2:391258/90‑1 (MQ=255)
tctTGCACCAGGGGTGCTTCGAGCATCTCACGGACAATTTTAGTGATACTGGCAGGAGCCAGTTGCGCCAGACGGGAAAGATCGATAcgc < 2:418353/90‑1 (MQ=255)
|
GTGCCAGGCTTCAGTTTCAACCACCAGCCCCACCGCCGGACGGCCACGGTTCCCCGCTTCTTTGATTTCCAGCTCTTGCACCAGGTGTGCTTCGAGCATCTCACGGACAATTTTAGTGATACTGGCAGGAGCCAGTTGCGCCAGACGGGAAAGATCGATACGC > NZ_CP009273/1662564‑1662726
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ 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
GCAGAGAAAGATAGTGCCAGGCTTCAGTTTCAACCACCAGCCCCACCGCCGGACGGCCACGGTTCCCCGCTTCTTTGATTTCCAGCTCTTGCACCAGGTGTGCTTCGAGCATCTCACGGACAATTTTAGTGATACTGGCAGGAGCCAGTTGCGCCAGACGGGAAAGATCGATACGCGAGACTGGACCAAGC > NZ_CP009273/1662551‑1662741
|
agagacagAGATAGTGCCAGGCTTCAGTTTCAACCACCAGCCCCACCGCCGGACGGCCACGGTTCCCCGCTTCTTTGATTTCCAGCTCTTGCACCAGGGG < SRR3721989.611887/92‑1 (MQ=60)
ATAGTGCCAGGCTTCAGTTTCAACCACCAGCCCCACCGCCGGACGGCCACGGTTCCCCGCTTCTTTGATTTCCAGCTCTTGCACCAGGGGTGCTTCGAGC < SRR3721989.234180/100‑1 (MQ=60)
AACCACCAGCCCCACCGCCGGACGGCCACGGTTCCCCGCTTCTTTGATTTCCAGCTCTTGCACCAGGGGTGCTTCGAGCATCTCACGGACAATTTTAGTG < SRR3721989.417267/100‑1 (MQ=60)
CCACCAGCCCCACCGCCGGACGGCCACGGTTCCCCGCTTCTTTGATTTCCAGCTCTTGCACCAGGGGTGCTTCGAGCATCTCACGGACAATTTTAGTGAT > SRR3721989.399177/1‑100 (MQ=60)
CCAGCCCCACCGCCGGACGGCCACGGTTCCCCGCTTCTTTGATTTCCAGCTCTTGCACCAGGGGTGCTTCGAGCATCTCACGGACAATTTTAGTGATACT < SRR3721989.369903/100‑1 (MQ=60)
GCTTCTTTGATTTCCAGCTCTTGCACCAGGGGTGCTTCGAGCATCTCACGGACAATTTTAGTGATACTGGCAGGGGCCAGTTGCGCCAGACGGGAAAGAT > SRR3721989.582806/1‑100 (MQ=60)
CACCAGGGGTGCTTCGAGCATCTCACGGACAATTTTAGTGATACTGGCAGGAGCCAGTTGCGCCAGACGGGAAAGATCGATACtgtctcttatacacatc > SRR3721989.133705/1‑83 (MQ=60)
|
GCAGAGAAAGATAGTGCCAGGCTTCAGTTTCAACCACCAGCCCCACCGCCGGACGGCCACGGTTCCCCGCTTCTTTGATTTCCAGCTCTTGCACCAGGTGTGCTTCGAGCATCTCACGGACAATTTTAGTGATACTGGCAGGAGCCAGTTGCGCCAGACGGGAAAGATCGATACGCGAGACTGGACCAAGC > NZ_CP009273/1662551‑1662741
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
