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 |
|
A12 F1 I2 R1
|
766 |
55.6 |
2631458 |
94.7% |
2491990 |
109.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,769,478 |
(G)7→9 |
coding (405/1113 nt) |
ydiK → |
UPF0118 family inner membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,769,471 | 1 | . | G | 95.8%
| 75.6
/ ‑3.1
| 24 | coding (398/1113 nt) | ydiK | UPF0118 family inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base G (15/8); total (15/9) |
| Fisher's exact test for biased strand distribution p-value = 3.75e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.93e-01 |
| * | NC_000913 | 1,769,471 | 2 | . | G | 91.7%
| 76.5
/ 0.4
| 24 | coding (398/1113 nt) | ydiK | UPF0118 family inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base . (1/1); new base G (14/8); total (15/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.34e-01 |
TATCGTCGACGGCAGCGGCCCGCTAATTAAAGCCATTTCCAGCGGTGACATGACGTTACCCGATCTGGCGTGGCTTAATACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTG‑CTGG‑ATAT‑‑GGGGGGGAC‑GGCGATCATGGCGAAAGTCCGCCCTTATATTGGCACCACCACCACCTGGTTCGTTGGGCAGGCGGCGCATATCGGGCGCTTTATGGTGCATTGTGCGCTGATGCTTCTCTTCAGTGCCCT > NC_000913/1769337‑1769600
||
tATCGTCGACGGCAGCGGCCCGCTAATTAAAGCCATTTCCAGCGGTGACATGACGTTACCCGATCTGGCGTGGCTTAATACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTG‑CTGG‑ATAT‑‑gggg < 2:525801/139‑1 (MQ=255)
tcgtcgACGGCAGCGGCCCGCTAATTAAAGCCATTTCCAGCGGTGACATGACGTTACCCGATCTGGCGTGGCTTAATACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTG‑CTGG‑ATAT‑‑gggggg > 1:648859/1‑139 (MQ=255)
tttCCAGCGGTGACATGACGTTACCCGATCTGGCGTGGCTTAATACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTG‑CTGG‑ATATGGGGGGGGGAC‑GGCGATCATGGCGAAAGTCCGCCCTtat > 2:661817/1‑139 (MQ=255)
tttCCAGCGGTGACATGACGTTACCCGATCTGGCGTGGCTTAATACCACTGCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTG‑CTGG‑ATATGGGGGGGGGAC‑GGCGATCATGGCGAAAGTCCGCCCTtat > 2:1169404/1‑139 (MQ=255)
cGGTGACATGACGTTACCCGATCTGGCGTGGCTTAATACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTG‑CTGG‑ATATGGGGGGGGGAC‑GGCGATCATGGCGAAAGTCCGCCCTTATATTGGca < 2:648859/139‑1 (MQ=255)
cGGTGACATGACGTTACCCGATCTGGCGTGGCTTAATACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTG‑CTGG‑ATATGGGGGGGGGAC‑GGCGATCATGGCGAAAGTCCGCCCTTATATTGGca > 2:513900/1‑139 (MQ=255)
ggATCTTGCCTGGCTTAATACCATTCCGGGTATTGGCGCGAAGCTGTAAGCAAGCTGGCACAACCTGCCTGGAATGG‑‑GGGGGGGAC‑GGCGATCATGGCGAAAGTCCGCCCTTATATTGGCACCACGACCACCTGGTTCg < 2:881492/138‑1 (MQ=255)
gCTTAATACTATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTG‑CTGG‑ATATG‑GGGGGGGGCGGGCGTTCTTGGCGAAAGTCCGCCCTTATTTTGGCACCACCACAACCTGGTTCGTTGGACAggccc > 1:881492/1‑137 (MQ=255)
aTTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTG‑CTGG‑ATAT‑‑ggg < 2:697938/56‑1 (MQ=255)
aTTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTG‑CTGG‑ATAT‑‑ggg > 1:697938/1‑56 (MQ=255)
ttCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTG‑CTGG‑ATATGGGGGGGGGAC‑GGCGATCATGGCGAAAGTCCGCCCTTATATTGGCACCACCACCACCTGGTTCGTTGGGCAGGCGGCGCATATCggg > 2:1217580/1‑139 (MQ=255)
tGGCGCGAAGCTGTATGCAGGCTGGCACAACTTG‑CTGG‑ATATGGGGGGGGGAC‑GGCGATCATGGCGAAAGTCCGCCCTTATATTGGCACCACCACCACCTGGTTCGTTGGGCAGGCGGCGCATATCGGGCGCTTTATgg > 2:936346/1‑139 (MQ=255)
tGTATGCAGGCTGGCACAACTTG‑CTGG‑ATATGGGGGGGGGAC‑GGCGATCATGGCGAAAGTCCGCCCTTATATTGGCACCACCACCACCTGGTTCGTTGGGCAGGCGGCGCATATCGGGCGCTTTATGGTGCATTGTgcg < 1:1217580/139‑1 (MQ=255)
tGCAGGCTGGCACAACTTG‑CTGG‑ATATGGGGGGGGGAC‑GGCGATCATGGCGAAAGTCCGCCCTTATATTGGCACCACCACCACCTGGTTCGTTGGGCAGGCGGCGCATATCGGGCGCTTTATGGTGCATTGTGCGCTGa < 1:431406/139‑1 (MQ=255)
aGGCTGGCACAACTTG‑CTGG‑ATATGGGGGGGGGAC‑GGCGATCATGGCGAAAGTc > 1:956567/1‑54 (MQ=255)
aGGCTGGCACAACTTG‑CTGG‑ATATGGGGGGGGGAC‑GGCGATCATGGCGAAAGTc < 2:956567/54‑1 (MQ=255)
gCTTGCACAACTTG‑CTGG‑ATATGGGGGGGGGAC‑GGCGATCATGGCGAAAGTCCGCCCTTATATTGGCACCACCACCACCTGGTTCGTTGGGCAGGCGGCGCATATCGGGCGCTTTATGGTGCATTGTGCGCTGATGCtt < 1:847374/139‑1 (MQ=255)
gCTGGCACAACTTG‑CTGG‑ATATGGGGGGGGGAC‑GGCGATCATGGCGAAAGTCCGCCCTTATATTGGCACCACCACCACCTGGTTCGTTGGGCAGGCGGCGCATATCGGGCGCt > 1:725732/1‑113 (MQ=255)
gCTGGCACAACTTG‑CTGG‑ATATGGGGGGGGGAC‑GGCGATCATGGCGAAAGTCCGCCCTTATATTGGCACCACCACCACCTGGTTCGTTGGGCAGGCGGCGCATATCGGGCGCt < 2:725732/113‑1 (MQ=255)
cTGGCACAACTTG‑CTGG‑ATATGGGGGGGGGAC‑GGCGATCATGGCGAAAGTCCGCCCTTATATTGGCACCACCACCACCTGGTTCGTTGGGCAGGCGGCGCATATCGGGCGCTTTATGGTGCATTGTGCGCTGATGCTtc > 1:1213146/1‑139 (MQ=255)
ggCACAACTTG‑CTGG‑ATATGGGGGGGGGAC‑GGCGATCATGGCGAAAGTCCGCCCTTATATTGGCACCACCACCACCTGGTTCGTTGGGCAGGCGGCGCATATCGGGCGCTTTATGGTGCATTGTGCGCTGATGCTtctc > 2:529216/1‑139 (MQ=255)
ggCACAACTTG‑CTGG‑ATATGGGGGGGGGAC‑GGCGATCATGGCGAAAGTCCGCCCTTATATTGGCACCACCACCACCTGGTTCGTTGGGCAGGCGGCGCATATCGGGCGCTTTATGGTGCATTGTGCGCTGATGCTtctc > 1:289879/1‑139 (MQ=255)
cactACTTG‑CTGG‑ATATGGGGGGGGGCC‑GGCGATCATGGCGAAAGTCCGCCCTTATATTGGCACCACCACCACCTGGTTCGTTGGGCAGGCGGCGCTTATCGGCCGCTTAATGGTGCATTGTGCGCTGATGCTTCTCtt > 2:847374/1‑139 (MQ=255)
cacaACTTG‑CTGG‑ATATGGGGGGGGGAC‑GGCGATCATGGCGAAAGTCCGCCCTTATATTGGcaccacc < 1:777333/68‑1 (MQ=255)
cacaACTTG‑CTGG‑ATATGGGGGGGGGAC‑GGCGATCATGGCGAAAGTCCGCCCTTATATTGGcaccacc > 2:777333/1‑68 (MQ=255)
cTGG‑ATATGGGGGGGGGAC‑GGCGATCATGGCGAAAGTCCGCCCTTATATTGGCACCACCACCACCTGGTTCGTTGGGCAgg < 2:446549/81‑1 (MQ=255)
cTGG‑ATATGGGGGGGGGAC‑GGCGATCATGGCGAAAGTCCGCCCTTATATTGGCACCACCACCACCTGGTTCGTTGGGCAgg > 1:446549/1‑81 (MQ=255)
cTGG‑ATATGGGGGGGGGAC‑GGCGATCATGGCGAAAGTCCGCCCTTATATTGGCACCACCACCACCTGGTTCGTTGGGCAGGCGGCGCATATCGGGCGCTTTATGGTGCATTGTGCGCTGATGCTTCTCTTCAGTGCCct > 1:169818/1‑139 (MQ=255)
||
TATCGTCGACGGCAGCGGCCCGCTAATTAAAGCCATTTCCAGCGGTGACATGACGTTACCCGATCTGGCGTGGCTTAATACCATTCCGGTGATTGGCGCGAAGCTGTATGCAGGCTGGCACAACTTG‑CTGG‑ATAT‑‑GGGGGGGAC‑GGCGATCATGGCGAAAGTCCGCCCTTATATTGGCACCACCACCACCTGGTTCGTTGGGCAGGCGGCGCATATCGGGCGCTTTATGGTGCATTGTGCGCTGATGCTTCTCTTCAGTGCCCT > NC_000913/1769337‑1769600
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
