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 I179 R1
|
182 |
40.3 |
1547118 |
96.8% |
1497610 |
120.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
535,507 |
A→G |
E302G (GAA→GGA) |
allB → |
allantoinase AllB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 535,507 | 0 | A | G | 92.3%
| 78.3
/ ‑0.1
| 26 | E302G (GAA→GGA) | allB | allantoinase AllB |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base G (13/11); total (14/12) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.44e-01 |
TCAGGACGTTACTTGTGAATCCTGCCCGCATTACTTTGTACTGGATACCGATCAGTTCGAAGAAATCGGTACTCTGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGAAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCCCGCCGGAAATGAAAGCCGGTAACATCATGAAAGCATGGGGCGGTATCGCCGGTCTGCAAAGCTGCATGGACGTGATGTT > NZ_CP009273/535379‑535639
|
tCAGGACGTTACTTGTGAATCCTGCCCGCATTACTTTGTACTGGATACCGATCAGTTCGAAGAAATCGGTACTCTGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGtt > 1:651652/1‑138 (MQ=255)
aGGACGTTACTTGTGAATCCTGCCCGCATTACTTTGTACTGGATACCGATCAGTTCGAAGAAATCGGTACTCTGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTaa > 2:590774/1‑139 (MQ=255)
gACGTTACTTGTGAATCCTGCCCGCATTACTTTGTACTGGATACCGATCAGTTCGAAGAAATCGGTACTCTGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACg < 1:590774/139‑1 (MQ=255)
cTTGTGAATCCTGCCCGCATTACTTTGTACTGGATACCGATCAGTTCGAAGAAATCGGTACTCTGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAAt < 1:251229/139‑1 (MQ=255)
aaTCCTGCCCGCATTACTTTGTACTGGATACCGATCAGTTCGAAGAAATCGGTACTCTGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTg > 1:595144/1‑139 (MQ=255)
cTTTGTACTGGATACCGATCAGTTCGAAGAAATCGGTACTCTGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCa < 1:739439/138‑1 (MQ=255)
cGATCAGTTCGAAGAAATCGGTACTCTGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCccgccg > 2:66122/1‑139 (MQ=255)
aTCAGTTCGAAGAAATCGGTACTCTGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCCCGCCgg > 2:50054/1‑138 (MQ=255)
aGTTCGAAGAAATCGGTACTCTGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGAAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCa > 2:614062/1‑118 (MQ=255)
aGTTCGAAAAAATCGGTACTCTGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGAAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCa < 1:614062/118‑1 (MQ=255)
aaTCGGTACTCTGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCCCGCCGGAAATGAAAGCCGGt < 1:66122/139‑1 (MQ=255)
tGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCCCGCCGGAAATGAAAGCCGGTAACATCATGa > 2:186013/1‑138 (MQ=255)
gCGAAGTTTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGgaa < 1:521983/55‑1 (MQ=255)
gCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGgaa > 2:521983/1‑55 (MQ=255)
ttCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGAc > 1:252749/1‑85 (MQ=255)
ttCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGAc < 2:252749/85‑1 (MQ=255)
cgATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGGCTGCCTGGTTTCCGACCACTCTCCATGCCCGCCGGAAATGAAAGCCGGTAACATCATGAAAGCATGGGGCGGTATCGc < 2:443504/139‑1 (MQ=255)
aTCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTcc < 1:516559/72‑1 (MQ=255)
aTCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTcc > 2:516559/1‑72 (MQ=255)
cgATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCCCGCCGGAAATGAAAGCCGGTAACATCATGAAAGCATGGGGCGGTATCGCCGGTCTg > 2:567618/1‑139 (MQ=255)
gAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCCCGCCGGAAATGAAAGCCGGTAACATCATGAAAGCATGGGGCGGTATCGCCGGTCTGCAAAg < 1:50054/137‑1 (MQ=255)
cAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCCCGCCGGAAATGAAAGCCGGTAACATCATGAAAGCATGGGGCGGTATCGCCGGTCTGCAAAGCTGCATg > 1:602170/1‑138 (MQ=255)
aaaGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCCCGCCGGAAATGAAAGCCGGTAACATCATGAAAGCATGGGGCGGTATCGCCGGTCTGCAAAg < 1:635416/128‑1 (MQ=255)
aaaGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCCCGCCGGAAATGAAAGCCGGTAACATCATGAAAGCATGGGGCGGTATCGCCGGTCTGCAAAg > 2:635416/1‑128 (MQ=255)
aaaGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCCCGCCGGAAATGAAAGCCGGTAACATCATGAAAGCATGGGGCGGTATCGCCGGTCTGCAAAGCTGCATGGACg < 2:651652/139‑1 (MQ=255)
tgtgGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCCCGCCGGAAATGAAAGCCGGTAACATCATGAAAGCATGGGGCGGTATCGCCGGTCTGCAAAGCTGCATGGACGTGATGtt > 1:427764/1‑139 (MQ=255)
tgGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCCCGCCGGAAATGAAAGCCGGTAAcat > 2:340555/1‑83 (MQ=255)
tgGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCCCGCCGGAAATGAAAGCCGGTAAcat < 1:340555/83‑1 (MQ=255)
|
TCAGGACGTTACTTGTGAATCCTGCCCGCATTACTTTGTACTGGATACCGATCAGTTCGAAGAAATCGGTACTCTGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGAAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCCCGCCGGAAATGAAAGCCGGTAACATCATGAAAGCATGGGGCGGTATCGCCGGTCTGCAAAGCTGCATGGACGTGATGTT > NZ_CP009273/535379‑535639
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CGTCAGGAAGGTCAGGACGTTACTTGTGAATCCTGCCCGCATTACTTTGTACTGGATACCGATCAGTTCGAAGAAATCGGTACTCTGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGAAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCCCGCCGGAAATGAAAGCCGGTAACATCATGAAAGCATGGGGCGGTATCGCCGGTCTGCAAAGCTGCATGGACGTGATGTTC > NZ_CP009273/535368‑535640
|
CGTCAGGAAGGTCAGGACGTTACTTGTGAATCCTGCCCGCATTACTTTGTACTGGATACCGATCAGTTCGAAGAAATCGGTACTCTGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTT > SRR3722133.660150/1‑150 (MQ=60)
tttttttcaagcagaagacggcatacgatatctagtacggtctcgtgggctgggagatgtgtataagagacagTCGGTACTCTGGCGAAGTTTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAAC < SRR3722133.529002/77‑1 (MQ=60)
taaacaccttttcgcgtccgctgtcggtggtggtgttttttttcaagcagaagacggcatacgatatctagtacggtctcgtgggctcggagatgtgtataagagacagCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGG < SRR3722133.92203/41‑1 (MQ=60)
GGACGTTACTTGTGAATCCTGCCCGCATTACTTTGTACTGGATACCGATCAGTTCGAAGAAATCGGTACTCTGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGAC < SRR3722133.598578/151‑1 (MQ=60)
CGTTACTTGTGAATCCTGCCCGCATTACTTTGTACTGGATACCGATCAGTTCGAAGAAATCGGTACTCTGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGC > SRR3722133.603000/1‑151 (MQ=60)
ACTTGTGAATCCTGCCCGCATTACTTTGTACTGGATACCGATCAGTTCGAAGAAATCGGTACTCTGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGG < SRR3722133.254651/151‑1 (MQ=60)
gacggcatacgaaatctagtccggtctcgtggcctcggagatgtgtataagagacagtTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCC < SRR3722133.523501/93‑1 (MQ=60)
ataagagacagggatcCCGATCAGTTCGAAAAAATCGGTACTCTGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGAAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCC < SRR3722133.622154/135‑1 (MQ=60)
ACTTTGTACTGGATACCGATCAGTTCGAAGAAATCGGTACTCTGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCC < SRR3722133.749004/150‑1 (MQ=60)
AAATCGGTACTCTGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCCCGCCGGAAATGAAAGCCGGTAACATCATGAA < SRR3722133.66959/151‑1 (MQ=60)
agatctagtacggtctcgtgggctcggagatgtgtataagagacagAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCCCGCCGGAAATGAAAGCCGGTAACATCATGAAAGCAT < SRR3722133.345336/105‑1 (MQ=60)
CTGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCtgtctcttatacacatctccgagcccacgagaccgtact > SRR3722133.256189/1‑108 (MQ=60)
ATCTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCCCGCCGGAAATGAAAGCCGGTAACATCATGAAAGCATGGGGCGGTATCGCCGGTCTGCAAAGCTGCATGG > SRR3722133.610110/1‑150 (MQ=60)
GTGGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCCCGCCGGAAATGAAAGCCGGTAACATCATGAAAGCATGGGGCGGTATCGCCGGTCTGCAAAGCTGCATGGACG < SRR3722133.643742/151‑1 (MQ=60)
GGAAAACCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCCCGCCGGAAATGAAAGCCGGTAACATCATGAAAGCATGGGGCGGTATCGCCGGTCTGCAAAGCTGCATGGACG < SRR3722133.50682/149‑1 (MQ=60)
CCAGAAAGGCATGTGGGGAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCCCGCCGGAAATGAAAGCCGGTAACATCATGAAAGCATGGGGCGGTATCGCCGGTCTGCAAAGCTGCATGGACGTGATGTTC > SRR3722133.433634/1‑151 (MQ=60)
|
CGTCAGGAAGGTCAGGACGTTACTTGTGAATCCTGCCCGCATTACTTTGTACTGGATACCGATCAGTTCGAAGAAATCGGTACTCTGGCGAAGTGTTCACCGCCGATCCGCGATCTGGAAAACCAGAAAGGCATGTGGGAAAAACTGTTTAACGGTGAAATCGACTGCCTGGTTTCCGACCACTCTCCATGCCCGCCGGAAATGAAAGCCGGTAACATCATGAAAGCATGGGGCGGTATCGCCGGTCTGCAAAGCTGCATGGACGTGATGTTC > NZ_CP009273/535368‑535640
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
