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 |
|
A25 F999 I0 R1
|
111 |
24.8 |
2365438 |
97.5% |
2306302 |
48.6 |
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 transporter YifK |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,980,951 | 1 | . | G | 97.2%
| 135.2
/ ‑2.5
| 36 | coding (65/1386 nt) | yifK | putative transporter YifK |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base G (23/12); total (24/12) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.32e-01 |
CAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCT‑GGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGT > NC_000913/3980903‑3980994
|
cAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCt < 1:1265920/49‑1 (MQ=255)
cAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCt < 1:1272026/49‑1 (MQ=255)
agagCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCT‑g > 1:2167796/1‑49 (MQ=255)
agagCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCT‑g > 1:199553/1‑49 (MQ=255)
gCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCT‑gggg > 1:2084555/1‑49 (MQ=255)
gCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCT‑gggg < 1:772234/49‑1 (MQ=255)
tACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCT‑gggggg > 1:935400/1‑49 (MQ=255)
aCAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCT‑ggggggg > 1:1390131/1‑48 (MQ=255)
gTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCTGGGGGGGCACCa > 1:127504/1‑49 (MQ=39)
gggCTGGAAGCTCGACATATCGAACTCATCGCCCTGGGGGGGCACCAtt > 1:2266959/1‑49 (MQ=39)
gggCTGGAAGCTCGACATATCGAACTCATCGCCCTGGGGGGGCACCAtt > 1:905910/1‑49 (MQ=39)
ggCTGGAAGCTCGACATATCGAACTCATCGCCCTGGGGGGGCACCATTg > 1:1011542/1‑49 (MQ=39)
ggCTGGAAGCTCGACATATCGAACTCATCGCCCTGGGGGGGCACCATTg > 1:1168413/1‑49 (MQ=39)
gCTGGAAGCTCGACATATCGAACTCATCGCCCTGGGGGGGCACCATTgg > 1:244327/1‑49 (MQ=39)
cTGGAAGCTCGACATATCGAACTCATCGCCCTGGGGGGGCACCATTGGc > 1:1568914/1‑49 (MQ=255)
tGGAAGCTCGACATATCGAACTCATCGCCCTGGGGGGGCACCATTGGCg > 1:378706/1‑49 (MQ=255)
tGGAAGCTCGACATATCGAACTCATCGCCCTGGGGGGGCACCATTGGCg > 1:1237418/1‑49 (MQ=255)
ggAAGCTCGACATATCGAACTCATCGCCCTGGGGGGGCACCATTGGCGt > 1:1585665/1‑49 (MQ=255)
ggAAGCTCGACATATCGAACTCATCGCCCTGGGGGGGCACCATTGGCGt > 1:207570/1‑49 (MQ=255)
gAAGCTCGACATATCGAACTCATCGCCCTGGGGGGGCACCATTGGCGt < 1:917027/48‑1 (MQ=255)
gAAGCTCGACATATCGAACTCATCGCCCTGGGGGGGCACCATTGGCGTc < 1:1287729/49‑1 (MQ=255)
aaGCTCGACATATCGAACTCATCGCCCT‑GGGGGGCACCATTGGCGTCgg > 1:65256/1‑49 (MQ=255)
gCTCGACATATCGAACTCATCGCCCTGGGGGGGCACCATTGGCGTCGGc < 1:1353890/49‑1 (MQ=39)
tCGACATATCGAACTCATCGCCCTGGGGGGGCACCATTGGCGTCGGCCt > 1:378888/1‑49 (MQ=39)
aCATATCGAACTCATCGCCCTGGGGGGGCACCATTGGCGTCGGCTTGtt > 1:893881/1‑49 (MQ=38)
aCATATCGAACTCATCGCCCTGGGGGGGCACCATTGGCGTCGGCCTGtt < 1:1404821/49‑1 (MQ=39)
cATATCGAACTCATCGCCCTGGGGGGGCACCATTGGCGTCGGCCTGttt < 1:1812073/49‑1 (MQ=39)
atatCGAACTCATCGCCCTGGGGGGGCACCATTGGCGTCGGCCTGTTTa > 1:956624/1‑49 (MQ=39)
tatCGAACTCATCGCCCTGGGGGGGCACCATTGGCGTCGGCCTGTTTAt > 1:1007122/1‑49 (MQ=39)
atCGAACTCATCGCCCTGGGGGGGCACCATTGGCGTCGGCCTGTTTATg > 1:1978130/1‑49 (MQ=39)
tCGAACTCATCGCCCTGGGGGGGCACCATTGGCGTCGGCCTGTTTATg < 1:2070445/48‑1 (MQ=39)
gAACTCATCGCCCTGGGGGGGCACCATTGGCGTCGGCCTGTTTATgggg > 1:413186/1‑49 (MQ=39)
aaCTCATCGCCCTGGGGGGGCACCATTGGCGTCGGCCTGTTTATggggg < 1:1435557/49‑1 (MQ=39)
aCTCATCGCCCTGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGgc > 1:2262861/1‑49 (MQ=39)
aCTCATCGCCCTGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGgc < 1:1638520/49‑1 (MQ=39)
aCTCATCGCCCTGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGgc < 1:1085800/49‑1 (MQ=39)
tCATCGCCCTGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGgccg > 1:1761356/1‑49 (MQ=39)
cATCGCCCTGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGgccgc > 1:1868281/1‑49 (MQ=39)
aTCGCCCTGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGgccgcc < 1:27793/49‑1 (MQ=39)
aTCGCCCTGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGgccgcc < 1:1645764/49‑1 (MQ=39)
aTCGCCCTGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGgccgc > 1:2181191/1‑48 (MQ=39)
aTCGCCCTGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGgccgc > 1:28769/1‑48 (MQ=39)
aTCGCCCTGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGgccgc > 1:809759/1‑48 (MQ=39)
gCCCTGGGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGt < 1:747660/49‑1 (MQ=39)
|
CAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCT‑GGGGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGT > NC_000913/3980903‑3980994
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
