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 |
|
A6 F1 I1 R1
|
750 |
51.0 |
2595496 |
93.6% |
2429384 |
106.4 |
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 | 86.4%
| 126.0
/ 13.9
| 45 | 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 . (6/0); new base C (16/22); total (23/22) |
| Fisher's exact test for biased strand distribution p-value = 2.11e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AAGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑C‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGG > NC_000913/2767300‑2767571
|
aaGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑aa > 2:985627/1‑139 (MQ=255)
gCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑c < 2:213203/139‑1 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑ctct > 2:332298/1‑136 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑cccc > 1:885719/1‑139 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑cccc > 1:49216/1‑139 (MQ=255)
ttttGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑aa > 2:940252/1‑130 (MQ=255)
ttttGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑aa < 1:940252/130‑1 (MQ=255)
ttGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑cccc‑ccctca < 1:985627/139‑5 (MQ=255)
gTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑Tcaca < 2:885719/139‑1 (MQ=255)
ccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTc < 1:1188931/139‑1 (MQ=255)
ccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTc < 2:49216/139‑1 (MQ=255)
ccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTc < 1:419532/139‑1 (MQ=255)
cGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑CACAAC‑CC‑TCACaaactac > 2:481120/1‑134 (MQ=255)
ccAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAac < 1:500837/139‑1 (MQ=255)
cAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑C‑CCCCACC‑TCAAAAAGCCCTGCATAGGGAaca > 2:624354/1‑139 (MQ=255)
aGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAac > 2:96543/1‑136 (MQ=255)
aGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAac < 1:96543/136‑1 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAAA‑C‑ACAC‑CC‑TCGCAACGTCCTGCAAAGAGAAGACGTTTTACCCagtg > 1:757561/1‑139 (MQ=255)
aTTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCa < 1:557320/139‑1 (MQ=255)
ctctTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAAA‑A‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGAACCCACGACTa > 2:226339/1‑139 (MQ=255)
ccAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTaaa < 1:624354/139‑1 (MQ=255)
aGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTGCCCCCCCTTTAAACt < 1:1170050/139‑1 (MQ=255)
gTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACtt < 1:927622/139‑1 (MQ=255)
tataGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAACACGTTTTcccc > 2:47362/1‑101 (MQ=255)
tataGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAACACGTTTTcccc < 1:47362/101‑1 (MQ=255)
aaTTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAac > 2:8085/1‑85 (MQ=255)
aaTTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAac < 1:8085/85‑1 (MQ=255)
cGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑C‑CCCC‑CCAACAAAACGTCTTGCATAGCAAACACGTTTTCCCCTGTTCACCCACGTCCAAATTTCAATCCCTTATAACTTCCCAATAATg > 2:927622/1‑139 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAAA‑C‑ACCC‑CC‑TCACAACGTCCTGCATATGTAACACGTTTTCACCTGTACACCCACGACTAAATTTACCTCCCGTTAAACATATAaataattt > 2:757071/1‑137 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACACCGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCTCCCCCTTTAACCTTCTCAATAATGt > 1:868520/1‑139 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTc < 2:155137/67‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTc > 1:155137/1‑67 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAac < 2:1188833/80‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAac > 1:1188833/1‑80 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAACACGtttt > 2:867931/1‑87 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAACACGtttt < 1:867931/87‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAACACGTTTTcc < 1:557683/89‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAACACGTTTTcc > 2:557683/1‑89 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑C‑CCCC‑CC‑TCCCAACGTCCTGCATAGGGAACACGGTTTCCCCCTTTCCCCCACCACTAACTTTCCCCCCTCTTAAAACTCTTCATAATGTc > 2:1188477/1‑139 (MQ=255)
gTCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGAATAGGGAACACGGTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTCCTCAATAATGTCACCAATTTTCTGGAAATCCTatg > 2:1244509/1‑139 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTc < 2:116873/42‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTc > 1:116873/1‑42 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTc > 1:623633/1‑42 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTc < 2:623633/42‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCaat > 2:637667/1‑109 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCaat < 1:637667/109‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAAGTTCCCCCCCTTTAAACTGCTCCATAATGTCACCAATTTGCTGGAAAACCTttga > 1:777157/1‑139 (MQ=255)
tCAAATAGCATT‑AAGC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAACACGCTCACCCCTGGTCACCCACGACTAAATTTCCCCCCCCTTAAACTTCTAAATAATGCTACCAATTTTCTTGAATGCATAAGATGACTTTccc > 1:1097475/1‑139 (MQ=255)
aGCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTaaa < 1:1230772/139‑1 (MQ=255)
aGCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTaaa < 1:655786/139‑1 (MQ=255)
gCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTa > 2:1007039/1‑81 (MQ=255)
gCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTa < 1:1007039/81‑1 (MQ=255)
gCATT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTACTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAAt > 1:268076/1‑139 (MQ=255)
aTT‑AACC‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCACTAATGTCACCAATTTTCTGGAAACCCTATGATGTCTTTCCCGGAAAATgg > 2:826442/1‑139 (MQ=255)
|
AAGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑C‑CCCC‑CC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGG > NC_000913/2767300‑2767571
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
