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 F4 I96 R1
|
227 |
23.3 |
882352 |
98.0% |
864704 |
126.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,068,442 |
A→C |
G323G (GGT→GGG) |
rutA ← |
pyrimidine utilization protein A |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,068,442 | 0 | A | C | 95.7%
| 75.1
/ ‑5.6
| 23 | G323G (GGT→GGG) | rutA | pyrimidine utilization protein A |
| Reads supporting (aligned to +/- strand): ref base A (0/0); major base C (10/12); minor base G (0/1); total (10/13) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AGGTCGTCATCATGCCACCTCCTGAGTCAGCGCAGGTAGATGGGCGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCACCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCGCCGAAGTGGGATCGGCCATCTGAC > NZ_CP009273/1068310‑1068548
|
aGGTCGTCATCATGCCACCTCCTGAGTCAGCGCAGGTAGATGGGCGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAgg < 2:141578/138‑1 (MQ=255)
catcatGCCACCTCCTGAGTCAGCGCAGGTAGATGGGCGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTg > 1:231703/1‑139 (MQ=255)
atGCCACCTCCTGAGTCAGCGCAGGTAGATGGGCGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGAc < 2:5464/139‑1 (MQ=255)
aGCGCAGGTAGATGGGCGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATgcgcg < 2:240889/139‑1 (MQ=255)
aGCGCAGGTAGATGGGCGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATgcgcg < 1:306277/139‑1 (MQ=255)
cgcAGGTAGATGGGCGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATgcgcgc > 2:434697/1‑138 (MQ=255)
gTAGATGGGCGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACt < 2:231703/139‑1 (MQ=255)
gcgGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGaa > 1:237525/1‑139 (MQ=255)
cATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTaa < 1:233084/138‑1 (MQ=255)
cgTGGTTGAATGCGCCCGCCGAAGGTTTCGATTCCCGGCAGCAAATCGTCGCAGCTTAACAGCACGCCTTCGGCGCCAGGCACGCTTGCGATTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTcc < 1:175359/138‑1 (MQ=255)
aGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTcc < 1:434697/139‑1 (MQ=255)
gTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTaa > 2:163856/1‑133 (MQ=255)
gTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTaa < 1:163856/133‑1 (MQ=255)
gTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTccc > 2:438709/1‑139 (MQ=255)
cgcTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGt > 2:410860/1‑139 (MQ=255)
tCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCGCCGAAGTgg > 2:89845/1‑139 (MQ=255)
aaaTCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCGCCGAAGTGGGATCGGCCATCTGAc < 2:291551/139‑1 (MQ=255)
cACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCGCCGAAGTGGGATCGGc > 2:259257/1‑111 (MQ=255)
cACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCGCCGAAGTGGGATCGGc < 1:259257/111‑1 (MQ=255)
aCGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACt < 1:283052/69‑1 (MQ=255)
aCGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACt > 2:283052/1‑69 (MQ=255)
cGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCata < 2:201271/74‑1 (MQ=255)
cGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCata > 1:201271/1‑74 (MQ=255)
|
AGGTCGTCATCATGCCACCTCCTGAGTCAGCGCAGGTAGATGGGCGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCACCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCGCCGAAGTGGGATCGGCCATCTGAC > NZ_CP009273/1068310‑1068548
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 34 ≤ 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
GTTAAGGTCGTCATCATGCCACCTCCTGAGTCAGCGCAGGTAGATGGGCGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCACCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCGCCGAAGTGGGATCGGCCATCTGACGAACGTTGGTGTCAGTACCGGAGCGGGTATCTTTCTGACTT > NZ_CP009273/1068306‑1068589
|
GTTAAGGTCGTCATCATGCCACCTCCTGAGTCAGCGCAGGTAGATGGGCGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGC > SRR3722119.234141/1‑151 (MQ=60)
CAGCGCAGGTAGATGGGCGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCG < SRR3722119.309406/151‑1 (MQ=60)
GGTAGATGGGCGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAAC > SRR3722119.240010/1‑151 (MQ=60)
gaagacggcatacgagattcgccttagtctcgtgggctcggagatgtgtataagagacagAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCAT < SRR3722119.285984/91‑1 (MQ=60)
GCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATAT < SRR3722119.165535/150‑1 (MQ=60)
GCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATAT < SRR3722119.235540/150‑1 (MQ=60)
CCGTGGTTGAATGCGCCCGCCGAAGGTTTCGATTCCCGGCAGCAAATCGTCGCAGCTTAACAGCACGCCTTCGGCGCCAGGCACGCTTGCGATTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATG < SRR3722119.177158/151‑1 (MQ=60)
CAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATG < SRR3722119.439048/151‑1 (MQ=60)
gatgtgtataagagacaGAAGGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCGCCGAAGTGGGATCGGCCATCTGACGAA < SRR3722119.261941/134‑1 (MQ=60)
GGTTAACAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACActgcctcttatacacatctccgaccccacgagactaaggcgaatctcgtatgccgtcttctgcttgaaaaaaaaaataatgccagagttcatgcactactg > SRR3722119.304308/1‑50 (MQ=60)
CAGCACGCCTTCGGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCtgtctcttatacacatctccgagcccacgagactaaggcgaatctcgtatgccg > SRR3722119.203417/1‑97 (MQ=60)
GGCCCCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCGCCGAAGTGGGATCGGCCATCTGACGAACGTTGGTGTCAGTACCGGAGCGGGTATCTTTCTGACTT < SRR3722119.414969/151‑1 (MQ=60)
|
GTTAAGGTCGTCATCATGCCACCTCCTGAGTCAGCGCAGGTAGATGGGCGCGGCATTGCATCAGTGGTTGAATGCGCTCGCCGAAGGTTTCGATTCCCGACAGAAAATCGTCGAAGGTTAACAGCACGCCTTCGGCACCAGGCACGCTTGCGACTTCATCTAACATGCGCGCGACACTGGCGTAAGAACCGACTAACGTCCCCATATTGATGTTTACCGCCGAAGTGGGATCGGCCATCTGACGAACGTTGGTGTCAGTACCGGAGCGGGTATCTTTCTGACTT > NZ_CP009273/1068306‑1068589
|
| 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: ‑ |
