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 |
967,323 |
Δ1 bp |
coding (116/894 nt) |
ycbJ → |
YcbJ family phosphotransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 967,321 | 0 | A | . | 97.1%
| 144.9
/ ‑1.6
| 35 | coding (114/894 nt) | ycbJ | YcbJ family phosphotransferase |
| Reads supporting (aligned to +/- strand): ref base A (1/0); new base . (17/17); total (18/17) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.53e-01 |
AAGCCATTTACTGGGCGAAAAACTCAGTCGTATTGAGTGCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGGAAACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCATGCTGGCAAGAAG > NZ_CP009273/967231‑967407
|
aaGCCATTTACTGGGCGAAAAACTCAGTCGTATTGAGTGCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGGa > 1:789228/1‑91 (MQ=255)
aTTTACTGGGCGAAAAACTCAGTCGTATTGAGTGCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGGAAccca > 2:190278/1‑90 (MQ=255)
tttACTGGGCGAAAAACTCAGTCGTATTGAGTGCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCaa < 2:462878/91‑1 (MQ=255)
tACTGGGCGAAAAACTCAGTCGTATTGAGTGCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATg < 1:547112/91‑1 (MQ=255)
cTGGGCGAAAAACTCAGTCGTATTGAGTGCGTCAACGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCCGGG‑AACCCAATGcc > 1:7851/1‑91 (MQ=255)
tCAGTCGTATTGAGTGCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCaaga < 2:563596/91‑1 (MQ=255)
tCAGTCGTATTGAGTGCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCaaga < 2:229318/91‑1 (MQ=255)
ttGAGTGCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGt < 2:626912/91‑1 (MQ=255)
tGAGTGCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTa < 1:190278/91‑1 (MQ=255)
gTGCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGc > 2:981246/1‑91 (MQ=255)
gTGCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGc > 2:670261/1‑91 (MQ=255)
gCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGccc > 1:280928/1‑91 (MQ=255)
gCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGccc < 1:666706/91‑1 (MQ=255)
gCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGccc > 2:1070153/1‑91 (MQ=255)
cGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCg > 1:909968/1‑91 (MQ=255)
aTGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGaaaa > 1:1110398/1‑91 (MQ=255)
aaaaGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCaaga > 1:789714/1‑66 (MQ=255)
aaaaGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCaaga < 2:789714/66‑1 (MQ=255)
ggCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCAt < 2:100255/91‑1 (MQ=255)
ggCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCAt < 2:1110398/91‑1 (MQ=255)
gCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATg > 1:749394/1‑91 (MQ=255)
gTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGa < 1:658230/91‑1 (MQ=255)
ttGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCAt > 1:889952/1‑91 (MQ=255)
cAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCATGCTGGCaa < 2:909968/91‑1 (MQ=255)
cAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCATGCTGGCaa < 2:889952/91‑1 (MQ=255)
cAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCATGCTGGCaa < 1:555682/91‑1 (MQ=255)
cAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCATGCTGGCaa < 1:2067/91‑1 (MQ=255)
gCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCATGCTGGCaaga > 1:864280/1‑91 (MQ=255)
gCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCATGCTGGCaaga > 2:672622/1‑91 (MQ=255)
gCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCATGCTGGCaaga < 1:474044/91‑1 (MQ=255)
gCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCATGCTGGCaaga > 1:504281/1‑91 (MQ=255)
gCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCATGCTGGCaaga > 2:225541/1‑91 (MQ=255)
gCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCATGCTGGCaaga > 2:1114573/1‑91 (MQ=255)
gCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCATGCTGGCaa > 2:104023/1‑89 (MQ=255)
gCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCATGCTGGCaa < 1:104023/89‑1 (MQ=255)
cAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCATGCTGGCaagaag > 2:5465/1‑91 (MQ=255)
|
AAGCCATTTACTGGGCGAAAAACTCAGTCGTATTGAGTGCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGGAAACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCATGCTGGCAAGAAG > NZ_CP009273/967231‑967407
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AAGCCATTTACTGGGCGAAAAACTCAGTCGTATTGAGTGCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGGAAACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCATGCTGGCAAGAAGTGGGACTG > NZ_CP009273/967231‑967415
|
AAGCCATTTACTGGGCGAAAAACTCAGTCGTATTGAGTGCGTCAACGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCCGGG‑AACCCAATGCC > SRR3722125.7994/1‑101 (MQ=60)
TACTGGGCGAAAAACTCAGTCGTATTGAGTGCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGG < SRR3722125.558827/101‑1 (MQ=60)
CGTATTGAGTGCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCC > SRR3722125.286624/1‑101 (MQ=60)
GTATTGAGTGCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCG > SRR3722125.930129/1‑101 (MQ=60)
TGAGTGCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAA < SRR3722125.194004/101‑1 (MQ=60)
GAGTGCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAA > SRR3722125.1135413/1‑101 (MQ=60)
GCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACtgtctcttatacac > SRR3722125.806940/1‑87 (MQ=60)
GCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCC < SRR3722125.681068/101‑1 (MQ=60)
AGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATG > SRR3722125.765571/1‑101 (MQ=60)
GTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCAT < SRR3722125.672431/101‑1 (MQ=60)
GTTGTGGGCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCAT > SRR3722125.909645/1‑101 (MQ=60)
GCTTTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGctgtctcttatacacatctccgagcccacgagactaggcatgatctcgt > SRR3722125.708163/1‑52 (MQ=60)
TTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCATGCTGGCAAGA > SRR3722125.514965/1‑101 (MQ=60)
TTGTATGACAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCATGCTGGCAAGA > SRR3722125.883346/1‑101 (MQ=60)
CAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCATGCTGGCAAGAAGTGGGAC < SRR3722125.567569/101‑1 (MQ=60)
CAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCATGCTGGCAAGAAGTGGGAC < SRR3722125.2122/101‑1 (MQ=60)
CAGCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCATGCTGGCAAGAAGTGGGAC < SRR3722125.106001/101‑1 (MQ=60)
GCCAGGG‑AACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCATGCTGGCAAGAAGTGGGACTG < SRR3722125.484043/101‑1 (MQ=60)
|
AAGCCATTTACTGGGCGAAAAACTCAGTCGTATTGAGTGCGTCAATGAAAAAGCGGATACGGCGTTGTGGGCTTTGTATGACAGCCAGGGAAACCCAATGCCGTTAATGGCAAGAAGCTTTAGTACGCCCGGAAAAGCCCGACAACTGGCATGGAAAACCACCATGCTGGCAAGAAGTGGGACTG > NZ_CP009273/967231‑967415
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
