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 F1 I2 R1
|
765 |
46.1 |
2269152 |
93.8% |
2128464 |
105.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,767,445 |
(C)7→8 |
intergenic (+90/‑265) |
rnlB → / → yfjP |
CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, 50S ribosome‑binding GTPase family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,767,438 | 1 | . | C | 85.7%
| 56.5
/ 3.6
| 21 | intergenic (+83/‑272) | rnlB/yfjP | CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, 50S ribosome‑binding GTPase family protein |
| Reads supporting (aligned to +/- strand): ref base . (3/0); new base C (6/12); total (9/12) |
| Fisher's exact test for biased strand distribution p-value = 6.32e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01 |
AGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑C‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAAT > NC_000913/2767301‑2767569
|
aGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c > 2:89809/1‑139 (MQ=255)
ccTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑cc > 1:159942/1‑139 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑cc‑cc > 1:879641/1‑139 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑cc‑c > 2:851262/1‑138 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑cc‑c < 1:851262/138‑1 (MQ=255)
tgcctcCCGATGATGTACGCCAAGTCCTGTCAATGGA‑TTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CC‑CCCCTcaca < 2:189122/136‑1 (MQ=255)
tctcCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑cc‑ccc < 2:965466/131‑1 (MQ=255)
tctcCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑cc‑ccc > 1:965466/1‑131 (MQ=255)
tctcCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTGGAACCTC‑TCTTTCTAAAAGAACCAGTTTAGAATTCCCCCTTTTTGCATGATACTTAATTGTCCAAACAGATCAAATAGCATT‑AA‑c‑cc‑cccccccccaaa > 1:189122/1‑131 (MQ=255)
ccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CC‑CCCCTCACAACGTc < 2:545053/139‑1 (MQ=255)
ccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CC‑CCCCTCACAACGTc < 1:89809/139‑1 (MQ=255)
ccAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAac < 2:159942/139‑1 (MQ=255)
aGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGCTATTAACTTGTCCAATATGATCAAATAGCATTAAA‑G‑CC‑CTCCTCACAACGCACTGCATAGGGAACACg > 1:1038072/1‑139 (MQ=255)
tGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CC‑CCCCTcaca < 1:881506/113‑1 (MQ=255)
tGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CC‑CCCCTcaca > 2:881506/1‑113 (MQ=255)
tCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTccc < 2:879641/139‑1 (MQ=255)
aaaCTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGa < 2:927157/139‑1 (MQ=255)
cAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAAc < 2:919135/139‑1 (MQ=255)
gCCCTTTTGGCATGACATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCa < 1:85670/97‑1 (MQ=255)
gCCCTTTTGGCATGACATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCa > 2:85670/1‑97 (MQ=255)
ccTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTccc > 2:1030627/1‑88 (MQ=255)
ccTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTccc < 1:1030627/88‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CC‑CCCCTCACCACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTccc > 2:615419/1‑90 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTccc < 1:615419/90‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AA‑CACC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTTATCAATTTTCTGGAAATCCCatga > 2:1093042/1‑139 (MQ=255)
tCCAATATGATCAAATAGCATT‑AA‑C‑CCTCCTCTACCAACGGCGTGAATAAGGCACACGGTTTACCCACTCCAACGAAGACTACGTTGCCCCCCCTTTCAAGCTGTCAGTCATCGCAGGAATCTTCTGGTAATCCGataa > 2:1134491/1‑137 (MQ=255)
gCATT‑AACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTATAAACTTCTCAATAATGTAACCAATTTTCTGGAAATCCTATGATACCTTTCCCGGTAAAt > 1:754171/1‑139 (MQ=255)
aTT‑AACC‑CC‑CCCCTCACAACGTCCTGGATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTccc > 2:94179/1‑71 (MQ=255)
aTT‑AACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTccc < 1:94179/71‑1 (MQ=255)
|
AGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑C‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAAT > NC_000913/2767301‑2767569
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
