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 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
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 | 95.0%
| 133.2
/ ‑0.8
| 40 | *1158E (TAA→GAA) | bcsC | cellulose synthase complex outer membrane protein BcsC |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base C (16/22); total (17/23) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.49e-01 |
ATTGTCTCCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTACCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAACGTACGTAGAGC > NZ_CP009273/3678979‑3679144
|
aTTGTCTCCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTc < 2:893722/90‑1 (MQ=255)
aTTGTCTCCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTc < 1:152069/90‑1 (MQ=255)
aTTGTCTCCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTc < 1:880477/90‑1 (MQ=255)
aTTGTCTCCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTc < 2:573304/90‑1 (MQ=255)
aTTGTCTCCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTc < 2:721649/90‑1 (MQ=255)
aTTGTCTCCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTc < 2:817879/90‑1 (MQ=255)
ctcCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGt < 2:156670/90‑1 (MQ=255)
ctcCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGt > 1:864256/1‑90 (MQ=255)
ccccccGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTACCAGTCGGCGTaa < 2:458510/90‑1 (MQ=255)
ccGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTa < 2:838552/90‑1 (MQ=255)
aTCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCg > 1:576306/1‑90 (MQ=255)
gATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTgcg > 2:79294/1‑90 (MQ=255)
aTTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTgcgg < 2:676326/90‑1 (MQ=255)
ccgccCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGcggcggg > 2:543104/1‑89 (MQ=255)
ccgccCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGt > 2:804787/1‑90 (MQ=255)
ccgccCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGt > 1:413532/1‑90 (MQ=255)
cgccCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTa < 1:384378/90‑1 (MQ=255)
cgccCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTa < 2:553771/90‑1 (MQ=255)
cccGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTaaa < 2:726678/90‑1 (MQ=255)
aCCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGGGAATTCAAGTcc > 2:864400/1‑89 (MQ=255)
cccGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCAc > 1:162831/1‑90 (MQ=255)
gATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCAcccc > 2:477900/1‑89 (MQ=255)
gATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCt > 1:727623/1‑90 (MQ=255)
gATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTACCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCt > 1:1293/1‑90 (MQ=255)
aTCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTg > 2:15623/1‑90 (MQ=255)
aTCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTg > 1:864404/1‑90 (MQ=255)
cAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCAt > 1:645102/1‑90 (MQ=255)
cGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCcg < 1:69812/90‑1 (MQ=255)
cATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCcggcg > 1:803936/1‑90 (MQ=255)
aTTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCcggcgg < 2:864404/90‑1 (MQ=255)
ttAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCcggcggc < 1:15623/90‑1 (MQ=255)
gagagGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGaa < 2:115107/90‑1 (MQ=255)
agGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAAt < 2:511604/58‑1 (MQ=255)
agGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAAt > 1:511604/1‑58 (MQ=255)
agGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCcggcggcgg > 2:117623/1‑85 (MQ=255)
agGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCcggcggcgg < 1:117623/85‑1 (MQ=255)
ggCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAac < 1:672941/90‑1 (MQ=255)
gcgcTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAacg < 1:202474/90‑1 (MQ=255)
gcgcTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGAGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAacg < 2:763412/90‑1 (MQ=255)
aaaaCTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAACGTACGTAGAGc < 1:874215/90‑1 (MQ=255)
|
ATTGTCTCCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTACCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAACGTACGTAGAGC > NZ_CP009273/3678979‑3679144
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 28 ≤ 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
GCGACTTACGCGCAAATTGTCTCCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTACCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAACGTACGTAGAGCAGGAAATGGCT > NZ_CP009273/3678964‑3679155
|
gatgtgtataagagacagGTCTCCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCC < SRR3722072.314644/82‑1 (MQ=60)
CGCAAATTGTCTCCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGT > SRR3722072.879162/1‑100 (MQ=60)
ATTGTCTCCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGT < SRR3722072.895628/100‑1 (MQ=60)
ATTGTCTCCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGT < SRR3722072.154743/100‑1 (MQ=60)
CCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCG > SRR3722072.586599/1‑100 (MQ=60)
TCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGT > SRR3722072.421021/1‑100 (MQ=60)
CCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCtgtctcttatacacatctccgagcccacg > SRR3722072.579867/1‑71 (MQ=60)
CGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTC < SRR3722072.391249/100‑1 (MQ=60)
CCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCAC > SRR3722072.165662/1‑100 (MQ=60)
GAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCT > SRR3722072.740543/1‑100 (MQ=60)
GAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTACCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCT > SRR3722072.1336/1‑100 (MQ=60)
AGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTG > SRR3722072.879314/1‑100 (MQ=60)
TACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCAT > SRR3722072.656590/1‑100 (MQ=60)
ATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCG > SRR3722072.817965/1‑100 (MQ=60)
CGGCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAAT < SRR3722072.71112/100‑1 (MQ=60)
GCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCtgtctcttatacacatctccgagcccacgagacgtccgattatctcgtatgccgtcttctgctt > SRR3722072.367458/1‑36 (MQ=60)
GCATTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGtctcttatacacatctccg > SRR3722072.520805/1‑81 (MQ=60)
TTAAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAACGT < SRR3722072.15923/100‑1 (MQ=60)
AAGAGAGGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAACGTAC < SRR3722072.119787/100‑1 (MQ=60)
GGCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAACGTACGTAGAG < SRR3722072.684994/100‑1 (MQ=60)
GCGCTATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAACGTACGTAGAGC < SRR3722072.205965/100‑1 (MQ=60)
ATCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAACGTctgtctcttataca > SRR3722072.303029/1‑86 (MQ=60)
TCTGAAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAACGTACGTAGAGCAGGAAA > SRR3722072.261738/1‑100 (MQ=60)
AAAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAACGTACGTAGAGCAGGAAATGGC < SRR3722072.889268/100‑1 (MQ=60)
AAACTTCCCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAACGTACGTAGAGCtgtctcttata > SRR3722072.890690/1‑89 (MQ=60)
|
GCGACTTACGCGCAAATTGTCTCCCCCCGGAAATCCCAGATTGCCGCCCGAGTATACCCGATCGCAGCGGCATTAAGAGAGGCGCTATCTGAAAACTTACCAGTCGGCGTAAGGTATCAGCGGCTGCGGCGGTAAATCCATGTCACCCTGCCATCCGGCGGCGGAATAACGTACGTAGAGCAGGAAATGGCT > NZ_CP009273/3678964‑3679155
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
