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 |
|
A10 F1 I2 R1
|
757 |
38.1 |
1607544 |
96.5% |
1551279 |
117.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,980,957 |
(G)6→7 |
coding (71/1386 nt) |
yifK → |
putative APC family amino acid transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,980,951 | 1 | . | G | 96.0%
| 172.2
/ ‑0.8
| 50 | coding (65/1386 nt) | yifK | putative APC family amino acid transporter |
| Reads supporting (aligned to +/- strand): ref base . (2/0); new base G (25/23); total (27/23) |
| Fisher's exact test for biased strand distribution p-value = 4.93e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ATAACGATAACCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCT‑GGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTACCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCGGGCTGTTCGTCTTTTTCATCATGCGTTCAATGGGCGAAAT > NC_000913/3980836‑3981083
|
aTAACGATAACCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGc < 2:52396/139‑1 (MQ=255)
aTAACGATAACCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGc < 1:4055/139‑1 (MQ=255)
aTAACGATAACCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGc < 1:774179/139‑1 (MQ=255)
tAACGATAACCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGcc > 2:359876/1‑139 (MQ=255)
tAACGATAACCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGcc < 1:50674/139‑1 (MQ=255)
aCGATAACCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCAACATATTGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTg > 2:478789/1‑139 (MQ=255)
gATAACCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGtt > 1:423301/1‑139 (MQ=255)
tAACCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTa > 2:268316/1‑139 (MQ=255)
aCCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATg < 2:423301/139‑1 (MQ=255)
ggTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATgggg > 1:22287/1‑139 (MQ=255)
tAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATgggg > 1:150272/1‑137 (MQ=255)
tAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATgggg < 2:150272/137‑1 (MQ=255)
aaCACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGgcc > 2:623466/1‑139 (MQ=255)
aaCACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGgcc > 1:616926/1‑139 (MQ=255)
ccGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCa > 1:474933/1‑139 (MQ=255)
ccGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCa < 2:341261/139‑1 (MQ=255)
ggAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCCG‑GGGGG‑GCCCCATTGGCGTCGGCCTGTTTATGAGGGCCGCCAGt > 1:109781/1‑139 (MQ=255)
aaGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTAcc < 2:616926/139‑1 (MQ=255)
aaGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTAcc > 1:204026/1‑139 (MQ=255)
aacacGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGt > 2:449711/1‑97 (MQ=255)
aacacGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGt < 1:449711/97‑1 (MQ=255)
aacacGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTACCCTGAAATgggccgg > 2:499504/1‑139 (MQ=255)
cacGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTACCCTGAAATgggccgggc < 2:22287/139‑1 (MQ=255)
cacGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGCCGGCCTGTTTATGGGGGCCGCCAGTACCCTGAAATgggccgggc < 2:183377/139‑1 (MQ=255)
tttATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTACCCTGAAATGGGCCGGGCCATCCGTa > 2:74945/1‑139 (MQ=255)
tttATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTACCCTGAAATGGGCCGGGCCATCCGTa > 2:207361/1‑139 (MQ=255)
tttATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTACCCTGAAATGGGCCGGGCCATCCGTa > 1:364945/1‑139 (MQ=255)
aTGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTACCCTGAAATGGGCCGGGCCATCCGTAttg < 2:204026/139‑1 (MQ=255)
tGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTACCCTGAAATGGGCCGGGCCATCCGTAttgt < 1:74945/139‑1 (MQ=255)
ggCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCT‑ggggg‑gg > 2:586737/1‑69 (MQ=255)
ggCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCT‑ggggg‑gg < 1:586737/70‑2 (MQ=255)
gATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTAcc > 2:745821/1‑106 (MQ=255)
gATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTAcc < 1:745821/106‑1 (MQ=255)
gATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTACCCTGAAATGGGCCGGGCCATCCGTATTGTTGGcc > 2:25939/1‑139 (MQ=255)
gATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTACCCTGAAATGGGCCGGGCCATCCGTATTGTTGGcc < 1:207361/139‑1 (MQ=255)
agagCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGc < 2:740066/71‑1 (MQ=255)
agagCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGc > 1:740066/1‑71 (MQ=255)
agCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTACCCTGAAATgggccgggc < 1:362059/109‑1 (MQ=255)
agCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTACCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCg > 1:455731/1‑139 (MQ=255)
agCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTGATGGGGGCCGCCAGTACCCTGAAATgggccgggc > 2:362059/1‑109 (MQ=255)
agCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCT‑ggggg‑gg > 1:72401/1‑52 (MQ=255)
agCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCT‑ggggg‑gg < 2:72401/53‑2 (MQ=255)
cGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTACCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCGGGCTGTTc < 1:623466/139‑1 (MQ=255)
tGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGc > 1:645961/1‑59 (MQ=255)
tGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGc < 2:645961/59‑1 (MQ=255)
ggCTGGAGGCTCGACATATCGAACTCATTG‑CCCT‑GGGGGTGCACCATTGGCGTCGGCCTGTTGATGGGGGCCGCCAGTACCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCGGGCTGGTCGTCt > 1:526330/1‑139 (MQ=255)
gCTCGACATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTACCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCGGGCTGTTCGTCTTTTtcatc < 1:752745/139‑1 (MQ=255)
aCATATCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTACCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCGGGCTGTTCGTCTTTTTCATCATGCg < 2:455731/139‑1 (MQ=255)
atCGAACTCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTACCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCGGGCTGTTCGTCTTTTTCATCATGCGTTCa > 1:502106/1‑139 (MQ=255)
tCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTACCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCGGGCTGTTCGTCTTTTtcatc > 1:383330/1‑123 (MQ=255)
tCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTACCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCGGGCTGTTCGTCTTTTtcatc < 2:383330/123‑1 (MQ=255)
tCATCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTACCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCGGGCTGTTCGTCTTTTTCATCATGCGTTCAATGGGCg < 1:499504/139‑1 (MQ=255)
aTCG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTACCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCGGGCTGTTCGTCTTTTTCATCATGCGTTCAATGGGCGaa > 2:754216/1‑139 (MQ=255)
cG‑CCCTGGGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTACCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCGGGCTGTTCGTCTTTTTCATCATGCGTTCAATGGGCGAAAt > 2:15481/1‑139 (MQ=255)
|
ATAACGATAACCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCG‑CCCT‑GGGGG‑GCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTACCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCGGGCTGTTCGTCTTTTTCATCATGCGTTCAATGGGCGAAAT > NC_000913/3980836‑3981083
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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
