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 |
|
A2 F5 I181 R1
|
159 |
32.7 |
1279082 |
96.9% |
1239430 |
121.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
659,797 |
A→C |
S284A (TCG→GCG) |
rlpA ← |
endolytic peptidoglycan transglycosylase RlpA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 659,797 | 0 | A | C | 100.0%
| 61.8
/ NA
| 19 | S284A (TCG→GCG) | rlpA | endolytic peptidoglycan transglycosylase RlpA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (11/8); total (11/8) |
ATTTTGAGTTACGCGACCGGGGACGCCGAACTTCTGTCCCAGTTGCTGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGAGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAGTACACCAGGCGCTAAGGTCGTTGGTGCGC > NZ_CP009273/659675‑659925
|
aTTTTGAGTTACGCGACCGGGGACGCCGAACTTCTGTCCCAGTTGCTGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTc < 2:205198/139‑1 (MQ=255)
gcACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCt > 2:577096/1‑69 (MQ=255)
gcACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCt < 1:577096/69‑1 (MQ=255)
gCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCg > 1:470087/1‑139 (MQ=255)
aTCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCg > 2:450639/1‑139 (MQ=255)
gCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTg < 2:458875/139‑1 (MQ=255)
gCTTACGGCCCCAACTTGCTCCATAAAGTTGCCGCTGGCGGTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTGGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTg < 2:504695/139‑1 (MQ=255)
ttACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGcc > 1:306083/1‑139 (MQ=255)
aCGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGcc < 2:306083/137‑1 (MQ=255)
gCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGgt < 1:434844/54‑1 (MQ=255)
gCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGgt > 2:434844/1‑54 (MQ=255)
ccccGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAg > 1:451372/1‑139 (MQ=255)
cACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGa < 2:70257/82‑1 (MQ=255)
cACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGa > 1:70257/1‑82 (MQ=255)
tAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAGTACACCAGGCGCt > 2:415963/1‑137 (MQ=255)
tAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAGTACACCAGGCGCt > 2:332672/1‑137 (MQ=255)
tAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAGTACACCAGGCGCt > 1:15393/1‑137 (MQ=255)
ccGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAGTACACCAGGCGCTAAGGTCGTTg > 2:234933/1‑139 (MQ=255)
gcgcTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAGTACACCAGGCGCTAAGGTCGTTGGTgcgc < 1:415963/139‑1 (MQ=255)
|
ATTTTGAGTTACGCGACCGGGGACGCCGAACTTCTGTCCCAGTTGCTGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGAGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAGTACACCAGGCGCTAAGGTCGTTGGTGCGC > NZ_CP009273/659675‑659925
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AGACCGCGCCATTTTGAGTTACGCGACCGGGGACGCCGAACTTCTGTCCCAGTTGCTGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGAGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAGTACACCAGGCGCTAAGGTCGTTGGTGCGCCGAGGAAACCG > NZ_CP009273/659665‑659936
|
gaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCAC < SRR3722135.584707/91‑1 (MQ=60)
ttttttttcaagcagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGC < SRR3722135.440772/76‑1 (MQ=60)
GTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGG > SRR3722135.476428/1‑151 (MQ=60)
AGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCT > SRR3722135.310473/1‑151 (MQ=60)
ATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAGT > SRR3722135.457480/1‑151 (MQ=60)
GCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACctgtctcttatacacatctccgagcccacgagaccgtactagatctc > SRR3722135.71200/1‑104 (MQ=60)
GACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAGTACACCAGGCGCTA > SRR3722135.15600/1‑149 (MQ=60)
GGCGCTTTGCGCGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAGTACACCAGGCGCTAAGGTCGTTGGTGCGCCGAGGAAACCG < SRR3722135.421680/151‑1 (MQ=60)
|
AGACCGCGCCATTTTGAGTTACGCGACCGGGGACGCCGAACTTCTGTCCCAGTTGCTGTTGGTACTGTTGCGCACGAGCCTGATCGCTTACGGCCCCGACTTGCACCATAAAGTTGCCGCTGGCGCTTTGCGAGACGGCTTGCGGTGTCACCATTGCAGGCGAGGTTGCAGGCGTTGTCGACGGAGCTGTAACAACGGGCTGTGGCGCAGGCGTCGGTTCGCTGCCTTCCAGTACACCAGGCGCTAAGGTCGTTGGTGCGCCGAGGAAACCG > NZ_CP009273/659665‑659936
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
