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 |
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 | 98.0%
| 180.8
/ ‑3.4
| 50 | coding (65/1386 nt) | yifK | putative APC family amino acid transporter |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base G (26/23); total (26/24) |
| Fisher's exact test for biased strand distribution p-value = 4.80e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01 |
CATTTGCAACACTCGATGTACCCATAACGATAACCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑T‑GGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA‑CCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCGGGCTGTTCGTCTTTTTCATCATGCGTTCAATGGGCG > NC_000913/3980813‑3981079
|
cATTTGCAACACTCGATGTACCCATAACGATAACCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑t < 2:818030/139‑1 (MQ=255)
acTCGATGTACCCATAACGATAACCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑A‑gggggggcac > 1:894068/1‑135 (MQ=255)
cTCGATGTACCCATAACGATAACCGGTAACACCGGAAAGCATGCGAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑T‑gggggggcacc > 1:313911/1‑134 (MQ=255)
tGTACCCATAACGATAACCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTgg > 1:279804/1‑139 (MQ=255)
aTAACGATAACCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCAG‑GGGGGGCACCATTGGCGTCGGc < 2:894068/139‑1 (MQ=255)
aTAACGATAACCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGc < 1:1015300/139‑1 (MQ=255)
aTAACGATAACCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGc < 1:1291769/139‑1 (MQ=255)
tAACGATAACCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGcc > 2:528807/1‑139 (MQ=255)
tAACGATAACCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGc < 2:197355/138‑1 (MQ=255)
tAACGATAACCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGc > 1:197355/1‑138 (MQ=255)
aCGATAACCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTg > 1:1156969/1‑139 (MQ=255)
tAACCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTa > 1:351487/1‑139 (MQ=255)
ccGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGCGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCa < 2:596370/139‑1 (MQ=255)
ccGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCa < 2:279804/139‑1 (MQ=255)
ccGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCa < 2:106248/139‑1 (MQ=255)
aTGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA‑CCCTGa > 2:845275/1‑139 (MQ=255)
tGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑t < 1:94765/87‑1 (MQ=255)
tGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑t > 2:94765/1‑87 (MQ=255)
tGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAg < 2:428817/130‑1 (MQ=255)
tGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAg < 2:364767/130‑1 (MQ=255)
tGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAg > 1:428817/1‑130 (MQ=255)
tGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAg > 1:364767/1‑130 (MQ=255)
gCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAg > 2:176083/1‑129 (MQ=255)
gCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAg < 1:176083/129‑1 (MQ=255)
gCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA‑CCCTGaaa > 1:1195908/1‑139 (MQ=255)
aacacaacacGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑T‑ggggggg > 1:458222/1‑89 (MQ=255)
aacacaacacGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑T‑ggggggg < 2:458222/90‑2 (MQ=255)
cacGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA‑CCCTGAAATgggccgggc > 2:387320/1‑139 (MQ=255)
cacGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA‑CCCTGAAATgggccgggc > 1:845892/1‑139 (MQ=255)
gATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA‑CCCTGAAATGGGCCGGGCCATCCg > 1:514777/1‑139 (MQ=255)
tATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCg < 2:391026/84‑1 (MQ=255)
tATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCg > 1:391026/1‑84 (MQ=255)
tGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA‑CCCTGAAATGGGCCGGGCCATCCGTAttgt < 2:1195908/139‑1 (MQ=255)
gATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCg < 2:441210/80‑1 (MQ=255)
gATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCg > 1:441210/1‑80 (MQ=255)
cAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCAGCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA‑CCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTttat < 2:845892/139‑1 (MQ=255)
cAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGc > 2:548707/1‑77 (MQ=255)
cAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGc < 1:548707/77‑1 (MQ=255)
agCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA‑CCCTGAAATGGGCCGGGCCATCCGTAttgt > 2:790270/1‑121 (MQ=255)
agCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA‑CCCTGAAATGGGCCGGGCCATCCGTAttgt < 1:790270/121‑1 (MQ=255)
agCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA‑CCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCg > 2:185574/1‑139 (MQ=255)
agCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA‑CCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCg > 1:1194940/1‑139 (MQ=255)
agCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA‑CCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCg > 1:434034/1‑139 (MQ=255)
tGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAg > 1:393589/1‑79 (MQ=255)
tGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAg < 2:393589/79‑1 (MQ=255)
ggCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA‑CCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCGGGCTGTTCGTCt > 1:1063905/1‑139 (MQ=255)
gCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA‑cc < 2:1152390/80‑1 (MQ=255)
gCTGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA‑cc > 1:1152390/1‑80 (MQ=255)
tGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGc < 2:1253154/54‑1 (MQ=255)
tGGAAGCTCGACATATCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGc > 1:1253154/1‑54 (MQ=255)
atCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTACCCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCGGGCTGTTCGTCTTTTTCATCATGCGTTc > 1:136266/1‑139 (MQ=255)
atCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA‑CCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTatat < 2:892631/102‑1 (MQ=255)
atCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA‑CCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTatat > 1:892631/1‑102 (MQ=255)
tCGAACTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA‑CCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCGGGCTGTTCGTCTTTTTCATCATGCGTTCaa < 1:72570/139‑1 (MQ=255)
aaCTCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA‑CCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCGGGCTGTTCGTCTTTTTCATCATGCGTTCAATgg < 1:528807/139‑1 (MQ=255)
tCATCGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA‑CCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCGGGCTGTTCGTCTTTTTCATCATGCGTTCAATGGGCg < 1:845275/139‑1 (MQ=255)
cGCCC‑TGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA‑CCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCgg < 1:764374/100‑1 (MQ=255)
|
CATTTGCAACACTCGATGTACCCATAACGATAACCGGTAACACCGGAAAGCATGCAAACACAACACGAGGATTTATGGCAGATAACAAACCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCC‑T‑GGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA‑CCCTGAAATGGGCCGGGCCATCCGTATTGTTGGCCTATATCATCGCCGGGCTGTTCGTCTTTTTCATCATGCGTTCAATGGGCG > NC_000913/3980813‑3981079
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
