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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
568,752 |
A→G |
G71G (GGA→GGG) |
ybcO → |
DUF1364 domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 568,752 | 0 | A | G | 92.9%
| 33.0
/ ‑3.1
| 14 | G71G (GGA→GGG) | ybcO | DUF1364 domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (3/10); total (3/11) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01 |
TACGAAACCGCCAGACCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTAC > NZ_CP009273/568665‑568838
|
tACGAAACCGCCAGACCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGgta < 2:53965/90‑1 (MQ=255)
ccTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATgcgc < 1:92957/90‑1 (MQ=255)
gATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGGATGCGCGCt > 2:351413/1‑90 (MQ=255)
gCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCg < 2:409643/90‑1 (MQ=255)
ctgcctgcCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAacac > 1:440637/1‑90 (MQ=255)
gcctgccACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCg > 1:349616/1‑81 (MQ=255)
gcctgccACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCg < 2:349616/81‑1 (MQ=255)
cgccgcACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAgggg < 1:323454/90‑1 (MQ=255)
ccgcACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGt < 2:487146/90‑1 (MQ=255)
ccgcACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGt < 2:57468/90‑1 (MQ=255)
ttgttgACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGt < 2:511418/90‑1 (MQ=255)
cTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTa < 1:158164/90‑1 (MQ=255)
tGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTAc < 1:197606/90‑1 (MQ=255)
tGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTAc < 2:440637/90‑1 (MQ=255)
tGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTAc < 2:549684/90‑1 (MQ=255)
|
TACGAAACCGCCAGACCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTAC > NZ_CP009273/568665‑568838
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ 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
GCACCGGTACGAAACCGCCAGACCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATT > NZ_CP009273/568658‑568849
|
tcgtcggcagcgtcagatgtgtataagagacagCCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGC < SRR3722111.247703/67‑1 (MQ=60)
CCCCGGTACAAAACCGCCAGCCCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCA < SRR3722111.301941/100‑1 (MQ=60)
CACCGGTACGAAACCGCCAGACCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCA < SRR3722111.106768/100‑1 (MQ=60)
CCGGTACGAAACCGCCAGACCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAA < SRR3722111.249828/100‑1 (MQ=60)
CCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGT < SRR3722111.94101/100‑1 (MQ=60)
ATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACAC > SRR3722111.447259/1‑100 (MQ=60)
TGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAG > SRR3722111.354354/1‑100 (MQ=60)
CGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGG < SRR3722111.327759/100‑1 (MQ=60)
CTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACA < SRR3722111.160163/100‑1 (MQ=60)
TGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACAT < SRR3722111.200065/100‑1 (MQ=60)
GGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATT > SRR3722111.116128/1‑100 (MQ=60)
|
GCACCGGTACGAAACCGCCAGACCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATT > NZ_CP009273/568658‑568849
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
