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 I95 R1
|
196 |
14.2 |
808436 |
96.0% |
776098 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,679,062 |
A→C |
*1158E (TAA→GAA) |
bcsC ← |
cellulose synthase complex outer membrane protein BcsC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,679,062 | 0 | A | C | 100.0%
| 61.3
/ NA
| 19 | *1158E (TAA→GAA) | bcsC | cellulose synthase complex outer membrane protein BcsC |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (8/11); total (8/11) |
ATTGTCTCCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTACCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAACGTACGTAGAGCAGGA > NZ_CP009273/3678979‑3679148
|
aTTGTCTCCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAGACTTCCCAGTc < 2:331182/90‑1 (MQ=255)
tcCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTa < 1:56742/90‑1 (MQ=255)
ccccccGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTaa > 1:355068/1‑90 (MQ=255)
ccccGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAgg < 2:355068/90‑1 (MQ=255)
ccGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTa < 1:185904/90‑1 (MQ=255)
aTCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCg > 2:19662/1‑90 (MQ=255)
aTTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTgcgg < 1:184270/90‑1 (MQ=255)
cGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGATAAATc < 2:38577/90‑1 (MQ=255)
aGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCa > 2:401898/1‑90 (MQ=255)
aGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCa > 2:29740/1‑90 (MQ=255)
aTCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAAACCATGTCAccccg > 2:296612/1‑88 (MQ=255)
ttAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCcggcggc < 1:43058/90‑1 (MQ=255)
gagGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCAccc > 1:366235/1‑70 (MQ=255)
gagGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCAccc < 2:366235/70‑1 (MQ=255)
agGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGaa < 2:61529/87‑1 (MQ=255)
agGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGaa > 1:61529/1‑87 (MQ=255)
ggCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCCGCCATCCGGCGGCGGGATAac > 2:182818/1‑90 (MQ=255)
cTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAACGTACGTAGAGCAGGa < 1:401898/90‑1 (MQ=255)
cTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAACGTACGTAGAGCAGGa < 1:29740/90‑1 (MQ=255)
|
ATTGTCTCCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTACCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAACGTACGTAGAGCAGGA > NZ_CP009273/3678979‑3679148
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ 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
CAAATTGTCTCCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTACCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAACGTACGTAGAGCAGGAAATGGCTGGG > NZ_CP009273/3678976‑3679158
|
CAAATTGTCTCCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAA > SRR3722235.360179/1‑100 (MQ=60)
TCCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGC < SRR3722235.57376/100‑1 (MQ=60)
CCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTG < SRR3722235.188076/100‑1 (MQ=60)
ATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCC < SRR3722235.186416/100‑1 (MQ=60)
GGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCtgtctctta > SRR3722235.371508/1‑91 (MQ=60)
GCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAA > SRR3722235.62220/1‑100 (MQ=60)
TTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAACGT < SRR3722235.43527/100‑1 (MQ=60)
CTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAACGTACGTAGAGCAGGAAATGGCTGGG < SRR3722235.30080/100‑1 (MQ=60)
CTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAACGTACGTAGAGCAGGAAATGGCTGGG < SRR3722235.407695/100‑1 (MQ=60)
|
CAAATTGTCTCCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTACCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAACGTACGTAGAGCAGGAAATGGCTGGG > NZ_CP009273/3678976‑3679158
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
