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 |
|
A13 F999 I0 R1
|
92 |
76.2 |
6048880 |
97.1% |
5873462 |
49.6 |
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 | 97.9%
| 186.0
/ ‑2.7
| 47 | coding (65/1386 nt) | yifK | putative transporter YifK |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base G (18/28); total (19/28) |
| Fisher's exact test for biased strand distribution p-value = 4.04e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01 |
CCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCT‑GG‑GGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA > NC_000913/3980902‑3980995
|
ccAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCt < 1:3660391/50‑1 (MQ=255)
ccAGAGCTACAGCGTGGGCTGG‑AGCTCGACATATCGAACTCATCGCCCT‑g > 1:356379/1‑50 (MQ=38)
cAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCT‑g < 1:1791375/50‑1 (MQ=255)
agagCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCT‑gg < 1:4328323/50‑1 (MQ=255)
agagCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCT‑gg < 1:4780741/50‑1 (MQ=255)
agCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCT‑gg‑gg < 1:5062004/50‑1 (MQ=255)
agCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCT‑gg‑gg < 1:2109598/50‑1 (MQ=255)
agCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCT‑gg‑gg < 1:4438405/50‑1 (MQ=255)
cTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCT‑gg‑gggg < 1:2911877/50‑1 (MQ=255)
cTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCT‑gg‑gggg < 1:1170539/50‑1 (MQ=255)
cTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCT‑gg‑gggg > 1:4792671/1‑50 (MQ=255)
tACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCT‑gg‑ggggg > 1:470551/1‑49 (MQ=255)
aCAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCT‑gg‑ggggg > 1:1636366/1‑48 (MQ=255)
cAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCT‑gg‑gggggc < 1:2898910/49‑3 (MQ=255)
gTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCTGGG‑GGGGCACCAt < 1:4405100/50‑1 (MQ=255)
gTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCTGGG‑GGGGCACCAt > 1:2938950/1‑50 (MQ=255)
gTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCTGGG‑GGGGCACCAt > 1:1147411/1‑50 (MQ=255)
gTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCTGGG‑GGGGCACCAt > 1:3816467/1‑50 (MQ=255)
tGGGCTGGAAGCTCGACATATCGAACTCATCGCCCTGGG‑GGGGCACCAtt < 1:476944/50‑1 (MQ=255)
ggCTGGAAGCTCGACATATCGAACTCATCGCCCTGGG‑GGGGCACCATTg < 1:5897965/49‑1 (MQ=39)
gCTGGAAGCTCGACATATCGAACTCATCGCCCTGGG‑GGGGCACCATTGGc < 1:2783144/50‑1 (MQ=255)
cTGGAAGCTCGACATATCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCg < 1:5434231/50‑1 (MQ=255)
cTGGAAGCTCGACATATCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCg < 1:4566127/50‑1 (MQ=255)
tGGAAGCTCGACATATCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGt > 1:4926963/1‑50 (MQ=255)
tGGAAGCTCGACATATCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGt > 1:1905742/1‑50 (MQ=255)
tGGAAGCTCGACATATCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGt > 1:4529898/1‑50 (MQ=255)
gAAGCTCGACATATCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGt < 1:933205/48‑1 (MQ=255)
gAAGCTCGACATATCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGTc < 1:1047769/49‑1 (MQ=255)
gAAGCTCGACATATCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGTc < 1:1099047/49‑1 (MQ=255)
aaGCTCGACATATCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGTCgg > 1:5222819/1‑50 (MQ=255)
aaGCTCGACATATCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGTCgg < 1:917986/50‑1 (MQ=255)
aaGCTCGACATATCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGTCgg < 1:1083833/50‑1 (MQ=255)
aaGCTCGACATATCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGTCgg > 1:4116370/1‑50 (MQ=255)
gCTCGACATATCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGTCGGcc > 1:3818477/1‑50 (MQ=255)
gCTCGACATATCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGTCGGcc > 1:1579312/1‑50 (MQ=255)
cTCGACATATCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGTCGGCCt > 1:52066/1‑50 (MQ=255)
cGACATATCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGt > 1:3627928/1‑50 (MQ=255)
gACATATCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGtt < 1:4171502/50‑1 (MQ=255)
aCATATCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGttt < 1:3724877/50‑1 (MQ=255)
cATATCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGTTTa < 1:5176434/50‑1 (MQ=255)
cATATCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGTTTa > 1:1242815/1‑50 (MQ=255)
cATATCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGTTTa < 1:1155908/50‑1 (MQ=255)
atatCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGTTTAt < 1:1095453/50‑1 (MQ=255)
atatCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGTTTAt > 1:5395832/1‑50 (MQ=255)
tatCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGTTTATg < 1:5819192/50‑1 (MQ=255)
atCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGTTTATgg > 1:380194/1‑50 (MQ=255)
tCGAACTCATCGCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGTTTATggg > 1:2695830/1‑50 (MQ=255)
aCTCATCGCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGTTTATGGGGgcc < 1:3248566/50‑1 (MQ=255)
aCTCATCGCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGTTTATGGGGgcc > 1:4395527/1‑50 (MQ=255)
cTCATCGCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGTTTATGGGGgccg < 1:4107410/50‑1 (MQ=255)
cTCATCGCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGTTTATGGGGgccg < 1:4347142/50‑1 (MQ=255)
cATCGCCCT‑GGTGGGGCACCATTGGCGTCGGCCTGTTTATGGGGgccgc > 1:3527411/1‑49 (MQ=38)
aTCGCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGTTTATGGGGgccgcc < 1:935019/49‑1 (MQ=39)
aTCGCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCa < 1:570152/50‑1 (MQ=255)
aTCGCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCa < 1:2594350/50‑1 (MQ=255)
aTCGCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCa < 1:2805380/50‑1 (MQ=255)
aTCGCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCa < 1:4120967/50‑1 (MQ=255)
gCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGt < 1:2055919/49‑1 (MQ=39)
gCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGt < 1:5780600/49‑1 (MQ=39)
gCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGt < 1:3680464/49‑1 (MQ=39)
gCCCTGGG‑GGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTa > 1:3209573/1‑50 (MQ=255)
|
CCAGAGCTACAGCGTGGGCTGGAAGCTCGACATATCGAACTCATCGCCCT‑GG‑GGGGCACCATTGGCGTCGGCCTGTTTATGGGGGCCGCCAGTA > NC_000913/3980902‑3980995
|
| 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
