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 |
951,809 |
T→G |
T94P (ACC→CCC) |
ycaO ← |
30S ribosomal protein S12 methylthiotransferase accessory factor YcaO |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 951,809 | 0 | T | G | 95.0%
| 60.0
/ ‑3.3
| 20 | T94P (ACC→CCC) | ycaO | 30S ribosomal protein S12 methylthiotransferase accessory factor YcaO |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base G (8/11); total (8/12) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.79e-01 |
CAGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGCGCCGCTTTCT > NZ_CP009273/951726‑951895
|
cagcCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGcc < 1:74186/90‑1 (MQ=255)
ccTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCccagc > 2:268295/1‑90 (MQ=255)
tCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCa > 2:463942/1‑90 (MQ=255)
tCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCa > 1:92143/1‑90 (MQ=255)
cGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAagtagt < 1:126468/90‑1 (MQ=255)
ggTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAgtt < 2:442082/90‑1 (MQ=255)
gTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAgttggttg > 1:165664/1‑90 (MQ=255)
tttttCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTc > 2:187565/1‑90 (MQ=255)
ttCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGaa < 1:527761/90‑1 (MQ=255)
tGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATAtt < 1:463942/90‑1 (MQ=255)
tAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCg < 2:113018/90‑1 (MQ=255)
tAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCg < 1:496704/90‑1 (MQ=255)
aTGCACGAACGGACCGTTGGCGATGGGTTAGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAg < 2:102509/90‑1 (MQ=255)
ggACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCg > 1:572280/1‑66 (MQ=255)
ggACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCg < 2:572280/66‑1 (MQ=255)
gACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAgtt > 1:65523/1‑49 (MQ=255)
gACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAgtt < 2:65523/49‑1 (MQ=255)
tGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACGGGGTGCAGAAGCCAGcgccg > 2:19360/1‑90 (MQ=255)
tGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCAAAATATTCACCGAGTGCAGAAGCCAGcgccg < 1:19360/90‑1 (MQ=255)
tGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGCGCCGCTTTCt < 2:520291/90‑1 (MQ=255)
|
CAGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGCGCCGCTTTCT > NZ_CP009273/951726‑951895
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ 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
CAGACGGTCATCGAGCAGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGCGCCGCTTTCTTGGT > NZ_CP009273/951711‑951899
|
CAGACGGTCATCGAGCAGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGT > SRR3722111.592810/1‑100 (MQ=60)
CAGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAG < SRR3722111.75082/100‑1 (MQ=60)
TTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCA > SRR3722111.93278/1‑100 (MQ=60)
TTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTG > SRR3722111.167742/1‑100 (MQ=60)
CGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAG < SRR3722111.128053/100‑1 (MQ=60)
TTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCG < SRR3722111.536045/100‑1 (MQ=60)
TGGGATAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGC < SRR3722111.471011/100‑1 (MQ=60)
TAATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAG < SRR3722111.504347/100‑1 (MQ=60)
ATGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCtgtctcttataca > SRR3722111.581269/1‑87 (MQ=60)
TGCACGAACGGACCGTTGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACtgtctcttatacacatctgacgctgccgac > SRR3722111.66294/1‑70 (MQ=60)
TGGCGATGGGTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCAAAATATTCACCGAGTGCAGAAGCCAGCGCCGCTTTCTTGGT < SRR3722111.19595/100‑1 (MQ=60)
|
CAGACGGTCATCGAGCAGCCCTTCTGGCACATCGTCATTTTCGGTCAGTGGGAACCATTTTTCGTTGGGATAATGCACGAACGGACCGTTGGCGATGGTTTCGCCCAGCCAGAAGTCCGCAAAAAAGTAGTTGGTTGAGAGACGCTCGAAATATTCACCGAGTGCAGAAGCCAGCGCCGCTTTCTTGGT > NZ_CP009273/951711‑951899
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
