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 |
|
A2 F1 I1 R1
|
404 |
265.1 |
10478538 |
96.8% |
10143224 |
150.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
CP009974 |
1,920,735 |
T→C |
intergenic (‑364/+191) |
RPPX_08560 ← / ← RPPX_08565 |
16S ribosomal RNA/CoA‑transferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP009974 | 1,920,735 | 0 | T | C | 96.5%
| 11.3
/ ‑6.3
| 29 | intergenic (‑364/+191) | RPPX_08560/RPPX_08565 | 16S ribosomal RNA/CoA‑transferase |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (9/19); total (9/20) |
| 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 |
CTTGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTTGATCGTAGCCCTTACAGC‑‑A‑‑CCTTCCGAATCGTCTAACTCATTGAATCTCAAGGAGTTTGTCGTTCCGTTGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAATTTCAATAACC > CP009974/1920691‑1920869
|
cTTGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCgag > 2:2909454/1‑151 (MQ=2)
ttGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCgaga > 1:2206084/1‑151 (MQ=2)
ttGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCgaga > 2:3599450/1‑151 (MQ=2)
tGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGagag < 1:1142689/151‑1 (MQ=2)
tGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGagag < 1:4468949/151‑1 (MQ=2)
tGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGagag < 1:5105177/151‑1 (MQ=2)
ggAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAgg < 2:3963621/151‑1 (MQ=2)
gAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAggg < 2:4679501/151‑1 (MQ=2)
aaGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGc < 2:2764414/151‑1 (MQ=2)
aGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGC‑‑TTTCCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAATGGGGCGCATTATAAGGGGATTCGAGAGGGCg > 1:291619/1‑151 (MQ=2)
gcgcTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGt > 2:853324/1‑151 (MQ=2)
gcgcTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGt < 2:1535075/151‑1 (MQ=2)
gcTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCa > 2:922201/1‑151 (MQ=2)
gcTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCa > 1:4893535/1‑151 (MQ=2)
gcTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCa < 1:2901300/151‑1 (MQ=2)
cTGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCaa < 1:2631112/151‑1 (MQ=2)
tGTCAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAAc < 1:2830356/151‑1 (MQ=2)
cAACCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCtt < 2:4385350/151‑1 (MQ=11)
aaCCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCttt < 2:2429346/151‑1 (MQ=2)
aaCCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCttt < 2:2712193/151‑1 (MQ=2)
aaCCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCttt < 2:4417863/151‑1 (MQ=2)
aaCCATCATCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCttt > 2:5128702/1‑151 (MQ=2)
catcatCTCAACCGCTTTCGATCATTCGACCGTAGCTCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAAt < 2:418203/151‑1 (MQ=11)
catcatCTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAAt < 1:678600/151‑1 (MQ=2)
ctcgtctcGACCGCTTGCGAGCAGTTGATCGTAGCCCGTACAGC‑‑A‑‑CCTTCCGAATCGTCTAACTCGTTGAACCTCGAGTAGTGTGTCGTTCCGTTGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAAtt < 2:3382521/147‑1 (MQ=11)
atcatcTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAAtt < 1:3533745/151‑1 (MQ=2)
atcatcTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGAGTCGAGAGGGCGTCAACCTTTAAtt > 2:150845/1‑151 (MQ=2)
catcTCAACCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAATTTc < 1:4777970/151‑1 (MQ=2)
aCCGCTTTCGATCATTCGACCGTAGCCCCTCCAGCTTT‑‑CCTTTC‑ACTACT‑TAACTCATTGAATCTCAAGGAGTTTTTCGTTCCGATGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAATTTCAATAAcc < 2:4556945/151‑1 (MQ=11)
|
CTTGGAAGCGCTGTCAACCATCATCTCAACCGCTTTCGATCATTTGATCGTAGCCCTTACAGC‑‑A‑‑CCTTCCGAATCGTCTAACTCATTGAATCTCAAGGAGTTTGTCGTTCCGTTGTCGCTGGAAGTGGGGCGCATTATAAGGGGATTCGAGAGGGCGTCAACCTTTAATTTCAATAACC > CP009974/1920691‑1920869
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
