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 I230 R1
|
226 |
18.8 |
1048726 |
96.7% |
1014118 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,012,671 |
G→C |
G51A (GGC→GCC) |
ssnA → |
putative aminohydrolase SsnA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,012,671 | 0 | G | C | 90.9%
| 26.9
/ ‑2.6
| 11 | G51A (GGC→GCC) | ssnA | putative aminohydrolase SsnA |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base C (4/6); total (4/7) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.12e-01 |
ATATCGCCATCGAAAACGATGTGATTGTCGCTATCGGCGATGCCCTGACGCAACGCTACCCCGACGCCAGCTTCAAAGAGATGCATGGCCGGATTGTGATGCCAGGGATTGTCTGCTCGCACAACCATTTTTACTCGGGGCTTTCCCGCGGAATTATGGCAAACATCGC > NZ_CP009273/3012584‑3012752
|
atatCGCCATCGAAAACGATGTGATTGTCGCTATCGGCGATGCCCTGACGCAACGCTACCCCGACGCCAGCTTCAAAGAGATGCATGccc < 2:409267/90‑1 (MQ=255)
atatCGCCATCGAAAACGATGTGATTGTCGCTATCGGCGATGCCCTGACGCAACGCTACCCCGACGCCAGCTTCAAAGAGATGCATGccc < 2:413757/90‑1 (MQ=255)
cGCCATCGAAAACGATGTGATTGTCGCTATCGGCGATGCCCTGACGCAACGCTACCCCGACGCCAGCTTCAAAGAGATGCATGCCCGGAt > 2:139256/1‑90 (MQ=255)
cGCCATCGAAAACGATGTGATTGTCGCTATCGGCGATGCCCTGACGCAACGCTACCCCGACGCCAGCTTCAAAGAGATGCATGCCCGGAt > 2:373785/1‑90 (MQ=255)
tCGAAAACGATGTGATTGTCGCTATCGGCGATGCCCTGACGCAACGCTACCCCGACGCCAGCTTCAAAGAGATGCATGGCCGGATTGTGa < 2:171495/90‑1 (MQ=255)
aTGTGATTGTCGCTATCGGCGATGCCCTGACGCAACGCTACCCCGACGCCAGCTTCAAAGAGATGCATGccc < 1:312795/72‑1 (MQ=255)
aTGTGATTGTCGCTATCGGCGATGCCCTGACGCAACGCTACCCCGACGCCAGCTTCAAAGAGATGCATGccc > 2:312795/1‑72 (MQ=255)
cGGCGATGCCCTGACGCAACGCTACCCCGACGCCAGCTTCAAAGAGATGCATGCCCGGATTGTGATGCCAGGGATTGTCTGCTCGCACaa < 2:410609/90‑1 (MQ=255)
gCGATGCCCTGACGCAACGCTACCCCGACGCCAGCTTCAAAGAGATGCATGCCCGGATTGTGATGCCAGGGATTGTCTGCTCGCACAAcc < 2:144028/90‑1 (MQ=255)
gCGATGCCCTGACGCAACGCTACCCCGACGCCAGCTTCAAAGAGATGCATGCCCGGATTGTGATGCCAGGGATTGTCTGCTCGCACAAcc > 2:196982/1‑90 (MQ=255)
gACGCAACGCTACCCCGACGCCAGCTTCAAAGAGATGCATGCCCGGATTGTGATGCCAGGGATTGTCTGCTCGCACAACCATTTTTACTc < 1:139256/90‑1 (MQ=255)
gACGCAACGCTACCCCGACGCCAGCTTCAAAGAGATGCATGCCCGGATTGTGATGCCAGGGATTGTCTGCTCGCACAACCATTTTTACTc < 1:140217/90‑1 (MQ=255)
cccGACGCCAGCTTCAAAGAGATGCATGCCCGGATTGTGATGCCAGGGATTGTCTGCTCGCACAACCATTTTTACTCGGGGCTTTCCcgc < 2:462884/90‑1 (MQ=255)
ttCAAAGAGATGCATGCCCGGATTGTGATGCCAGGGATTGTCTGCTCGCACAACCATTTTTACTCGGGGCTTTCCCGCGGAATTATGGCa < 1:268366/90‑1 (MQ=255)
gaTGCATGCCCGGATTGTGATGCCAGGGATTGTCTGCTCGCACAACCATTTTTACTCGGGGCTTTCCCGCGGAATTATGGCAAACATCGc > 2:276509/1‑90 (MQ=255)
|
ATATCGCCATCGAAAACGATGTGATTGTCGCTATCGGCGATGCCCTGACGCAACGCTACCCCGACGCCAGCTTCAAAGAGATGCATGGCCGGATTGTGATGCCAGGGATTGTCTGCTCGCACAACCATTTTTACTCGGGGCTTTCCCGCGGAATTATGGCAAACATCGC > NZ_CP009273/3012584‑3012752
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ 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
ATATCGCCATCGAAAACGATGTGATTGTCGCTATCGGCGATGCCCTGACGCAACGCTACCCCGACGCCAGCTTCAAAGAGATGCATGGCCGGATTGTGATGCCAGGGATTGTCTGCTCGCACAACCATTTTTACTCGGGGCTTTCCCGCGGAATTATGGCAAACATCGCCCCTTGCCCG > NZ_CP009273/3012584‑3012762
|
agagacagATCGAAAACGATGTGATTGTCGCTATCGGCGATGCCCTGACGCAACGCTACCCCGACGCCAGCTTCAAAGAGATGCATGCCCGGATTGTGAT < SRR3722114.316137/92‑1 (MQ=60)
GACGCAACGCTACCCCGACGCCAGCTTCAAAGAGATGCATGCCCGGATTGTGATGCCAGGGATTGTCTGCTCGCACAACCATTTTTACTCGGGGCTTTCC < SRR3722114.140698/100‑1 (MQ=60)
GACGCAACGCTACCCCGACGCCAGCTTCAAAGAGATGCATGCCCGGATTGTGATGCCAGGGATTGTCTGCTCGCACAACCATTTTTACTCGGGGCTTTCC < SRR3722114.141665/100‑1 (MQ=60)
TTCAAAGAGATGCATGCCCGGATTGTGATGCCAGGGATTGTCTGCTCGCACAACCATTTTTACTCGGGGCTTTCCCGCGGAATTATGGCAAACATCGCCC < SRR3722114.271130/100‑1 (MQ=60)
GATGCATGCCCGGATTGTGATGCCAGGGATTGTCTGCTCGCACAACCATTTTTACTCGGGGCTTTCCCGCGGAATTATGGCAAACATCGCCCCTTGCCCG > SRR3722114.236547/1‑100 (MQ=60)
GATGCATGCCCGGATTGTGATGCCAGGGATTGTCTGCTCGCACAACCATTTTTACTCGGGGCTTTCCCGCAGAATTATGGCAAACATCGCCCCTTGCCCG > SRR3722114.44811/1‑100 (MQ=60)
|
ATATCGCCATCGAAAACGATGTGATTGTCGCTATCGGCGATGCCCTGACGCAACGCTACCCCGACGCCAGCTTCAAAGAGATGCATGGCCGGATTGTGATGCCAGGGATTGTCTGCTCGCACAACCATTTTTACTCGGGGCTTTCCCGCGGAATTATGGCAAACATCGCCCCTTGCCCG > NZ_CP009273/3012584‑3012762
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
