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 F5 I102 R1
|
278 |
39.1 |
2251254 |
95.8% |
2156701 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
757,924 |
T→C |
L316P (CTG→CCG) |
odhB → |
2‑oxoglutarate dehydrogenase complex dihydrolipoyllysine‑residue succinyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 757,924 | 0 | T | C | 96.3%
| 86.8
/ ‑3.4
| 27 | L316P (CTG→CCG) | odhB | 2‑oxoglutarate dehydrogenase complex dihydrolipoyllysine‑residue succinyltransferase |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (12/14); total (12/15) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.58e-01 |
CGATACCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTCCCTGATGTCTACGCCGATCATCAACCCGCCGCAGAGCGC > NZ_CP009273/757838‑758008
|
cGATACCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGAcc < 2:868659/91‑1 (MQ=255)
cGATACCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGAcc < 2:461492/91‑1 (MQ=255)
gATACCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCg < 1:277509/91‑1 (MQ=255)
gATACCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCg > 2:306821/1‑91 (MQ=255)
ccTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCggtggt < 2:860560/91‑1 (MQ=255)
tCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTaa > 1:17758/1‑91 (MQ=255)
tCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTaa > 1:579816/1‑91 (MQ=255)
ggCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTtcacc > 2:519480/1‑91 (MQ=255)
cATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTtcaccatcacc > 1:545723/1‑91 (MQ=255)
tCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCaa > 2:562010/1‑91 (MQ=255)
cGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAAc < 1:1000019/91‑1 (MQ=255)
aaaaTCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTTCACCATCACCAACGgtggtg < 1:263052/91‑1 (MQ=255)
aaaTCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGgtgt > 1:895360/1‑91 (MQ=255)
aaaTCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGgtgt > 1:691745/1‑91 (MQ=255)
cAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTc < 2:488541/91‑1 (MQ=255)
gagCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGtt < 2:36519/91‑1 (MQ=255)
gagCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGtt < 1:28486/91‑1 (MQ=255)
ggCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTCCCTg < 1:609168/91‑1 (MQ=255)
cGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTCCCTGATGTCTACGCCGa < 1:705449/91‑1 (MQ=255)
gTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTCCCTGATGTCTACGCCGat > 1:84120/1‑91 (MQ=255)
gTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTCCCTGATGTCTACGCCGat > 1:607786/1‑91 (MQ=255)
gTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTCCCTGATGTCTACGCCGat > 2:989981/1‑91 (MQ=255)
gCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTCCCTGATGTCTACGCCGATCATCaa < 1:993383/91‑1 (MQ=255)
gCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTCCCTGATGTCTACGCCGATCATCaa < 2:607786/91‑1 (MQ=255)
ttGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTCCCTGATGTCTACGCCGATCATCAACCCGCCGCagag > 1:765550/1‑91 (MQ=255)
gAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTCCCTGATGTCTACGCCGATCATCAACCCGCCGCAGAgcg < 1:997587/91‑1 (MQ=255)
aaGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTCCCTGATGTCTACGCCGATCATCACCCCGCCGCAGAgcgc < 2:69657/91‑1 (MQ=255)
|
CGATACCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTCCCTGATGTCTACGCCGATCATCAACCCGCCGCAGAGCGC > NZ_CP009273/757838‑758008
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GTTCTGCGTGATGTCGATACCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTCCCTGATGTCTACGCCGATCATCAACCCGCCGCAGAGCGCAATTCTGGGT > NZ_CP009273/757824‑758018
|
GTTCTGCGCGATGTCGATACCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCG > SRR3722125.551475/1‑101 (MQ=60)
GTCGATACCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAA > SRR3722125.592236/1‑101 (MQ=60)
GTCGATACCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAA > SRR3722125.18077/1‑101 (MQ=60)
GATACCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTT < SRR3722125.283122/101‑1 (MQ=60)
GCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACC > SRR3722125.557382/1‑101 (MQ=60)
ATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGT > SRR3722125.915172/1‑101 (MQ=60)
ATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGT > SRR3722125.706673/1‑101 (MQ=60)
CGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGTCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGCTGGTGTGT < SRR3722125.1022367/101‑1 (MQ=60)
AAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTC < SRR3722125.268360/101‑1 (MQ=60)
GAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTCCCTGATGTC < SRR3722125.28997/101‑1 (MQ=60)
GGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTCCCTGATGTCTACGC < SRR3722125.622285/101‑1 (MQ=60)
GTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGctgtctcttatacacatctccgagcccacgagactaggcatgatctcgtatgcc > SRR3722125.1083125/1‑47 (MQ=60)
GTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTCCCTGATGTCTACGCCGAT > SRR3722125.620872/1‑101 (MQ=60)
GTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTCCCTGATGTCTACGCCGAT > SRR3722125.85695/1‑101 (MQ=60)
CGTGACGGCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTCCCTGATGTCTACGCCGATCATCAACCC < SRR3722125.720664/101‑1 (MQ=60)
GCAAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTCCCTGATGTCTACGCCGATCATCAACCCGCCGCAG < SRR3722125.1015575/101‑1 (MQ=60)
AAGCTGACCGTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTCCCTGATGTCTACGCCGATCATCAACCCGCCGCAGAG > SRR3722125.782163/1‑101 (MQ=60)
GTTGAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTCCCTGATGTCTACGCCGATCATCAACCCGCCGCAGAGCGCAATTCT > SRR3722125.27285/1‑101 (MQ=60)
GAAGATCCGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTCCCTGATGTCTACGCCGATCATCAACCCGCCGCAGAGCGCAATTCTGGG < SRR3722125.1019875/101‑1 (MQ=60)
AATATCCGACCGGTGATATCTTCACCACCACCACGGGTGGTGTGTTCGGTTCCCTGATGTCTACGCCGATCATCAACCCGCCGCAGAGCGCAATTCTGGGT < SRR3722125.621443/101‑1 (MQ=60)
|
GTTCTGCGTGATGTCGATACCCTCGGCATGGCAGACATCGAGAAGAAAATCAAAGAGCTGGCAGTCAAAGGCCGTGACGGCAAGCTGACCGTTGAAGATCTGACCGGTGGTAACTTCACCATCACCAACGGTGGTGTGTTCGGTTCCCTGATGTCTACGCCGATCATCAACCCGCCGCAGAGCGCAATTCTGGGT > NZ_CP009273/757824‑758018
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 2 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
