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 |
|
A4 F21 I0 R1
|
1009 |
73.8 |
4146436 |
87.4% |
3623985 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,023,066 |
G→A |
21.3% |
P281S (CCA→TCA) |
ygiQ ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,023,066 | 0 | G | A | 21.3%
| 136.3
/ 32.3
| 66 | P281S (CCA→TCA) | ygiQ | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (22/29); new base A (7/7); total (30/36) |
| Fisher's exact test for biased strand distribution p-value = 7.64e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.05e-01 |
TATCGCCCTTCACTTTCTCGAAAGAAGGCAGCAACACGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACCGGTTTGTTATCCGCGCACGGCAAATC > minE/2022997‑2023135
|
tATCGCCCTTCACTTTCTCGAAAGAAGGCAGCAACACGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGGc > 1:2600894/1‑71 (MQ=255)
gCCCTTCACTTTCTCGAAAGAAGGCAGCAACACGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGGc < 1:823952/67‑1 (MQ=255)
ccTTCACTTTCTCGAAAGAAGGCAGCAACACGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACg < 1:3012931/71‑1 (MQ=255)
cTTCACTTTCTCGAAAGAAGGCAGCAACACGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGc < 1:1388442/67‑1 (MQ=255)
cACTTTCTCGAAAGAAGGCAGCAACACGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTa > 1:1352445/1‑71 (MQ=255)
cACTTTCTCGAAAGAAGGCAGCAACACGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGACTGCACGGTTa > 1:2541808/1‑71 (MQ=255)
aCTTTCTCGAAAGAAGGCAGCAACACGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTAc < 1:1144730/71‑1 (MQ=255)
tttCTCGAAAGAAGGCAGCAACACGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGACTGCACGGTTACgg > 1:3347261/1‑71 (MQ=255)
ttCTCGAAAGAAGGCAGCAACACGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTa > 1:1629731/1‑67 (MQ=255)
tctcGAAAGAAGGCAGCAACACGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGc < 1:3885346/70‑1 (MQ=255)
tctcGAAAGAAGGCAGCAACACGTAGGTTTTTTCCCAAGGTTTCGGGCGCGGTGACTGCAc < 1:4055204/61‑1 (MQ=255)
ctcGAAAGAAGGCAGCAACACGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCtt > 1:2276601/1‑71 (MQ=255)
tcGAAAGAAGGCAGCAACACGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGACt > 1:3305427/1‑55 (MQ=255)
gAAAGAAGGCAGCAACACGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGACTGCACGGTTACGGCttt < 1:1095598/69‑1 (MQ=255)
aagaagGCAGCAACACGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCt < 1:882374/71‑1 (MQ=255)
gcaACACGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCttt < 1:1733426/71‑1 (MQ=255)
aaCACGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCttttt > 1:2796147/1‑71 (MQ=255)
aaCACGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCttttt > 1:389415/1‑71 (MQ=255)
aaCACGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCttttt > 1:1923488/1‑71 (MQ=255)
acacGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTc > 1:2781405/1‑71 (MQ=255)
acGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACgg > 1:987542/1‑49 (MQ=255)
acGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACgg > 1:1731970/1‑49 (MQ=255)
acGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCgg > 1:2704954/1‑71 (MQ=255)
cGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCtttt < 1:2035812/66‑1 (MQ=255)
gTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTg > 1:137260/1‑71 (MQ=255)
tAGGTTTTTTCCCACGGTTTCGGGCGCGGTGACTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGc > 1:4033258/1‑71 (MQ=255)
ggTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACg < 1:523984/43‑1 (MQ=255)
ggTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCa > 1:2794086/1‑71 (MQ=255)
gTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGtt < 1:365742/39‑1 (MQ=255)
gTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGc < 1:2616308/57‑1 (MQ=255)
gTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCAc < 1:1207535/71‑1 (MQ=255)
gTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCAc > 1:1578675/1‑71 (MQ=255)
gTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCAc < 1:1676561/71‑1 (MQ=255)
gTTTTTTCCCACGGTTTCGGGCGCGGTGACTGCACGGTTACGGCTTTGGCtt < 1:2686594/52‑1 (MQ=255)
gTTTTTTCCCACGGTTTCGGGCGCGGTGACTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCAc < 1:1219331/71‑1 (MQ=255)
tttttCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACCg > 1:747411/1‑71 (MQ=255)
ttttCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACCgg > 1:1895443/1‑71 (MQ=255)
ttttCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACCg < 1:2671112/70‑1 (MQ=255)
ttttCCCACGGTTTCGGGCGCGGTGACTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACCgg > 1:2135010/1‑71 (MQ=255)
tttCCCACGGTTTCGGGCGCGGTGTCTGCACGGTTACGGCTTTGGCTTCCTGCttttt > 1:3113953/1‑58 (MQ=255)
tttCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCttttt > 1:1540899/1‑58 (MQ=255)
tttCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCttt > 1:3097804/1‑56 (MQ=255)
tttCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACCGGt > 1:112160/1‑71 (MQ=255)
tttCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACCGGt > 1:2927625/1‑71 (MQ=255)
ttCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACCGGt < 1:1325056/70‑1 (MQ=255)
ttCCCACGGTTTCGGGCGCGGTGACTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACCGGtt > 1:1188241/1‑71 (MQ=255)
cccACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCgg < 1:208248/58‑1 (MQ=255)
cccACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACCGGttt < 1:1813449/70‑1 (MQ=255)
cccACGGTTTCGGGCGCGGTGACTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACCGGttt < 1:3152936/70‑1 (MQ=255)
ccACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACCGGTTTg < 1:2568901/70‑1 (MQ=255)
ccACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACAGGTTTg < 1:2475442/70‑1 (MQ=255)
cACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGc < 1:787154/35‑1 (MQ=255)
cACGGTTTCGGGCGCGGTGACTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACCGGTTTg < 1:1927500/69‑1 (MQ=255)
aCGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTcc > 1:3392644/1‑44 (MQ=255)
aCGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACCg < 1:3160667/63‑1 (MQ=255)
aCGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACCGGTTTGTTa < 1:1749523/71‑1 (MQ=255)
ggTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACCg < 1:1866618/61‑1 (MQ=255)
gTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCt < 1:2623200/38‑1 (MQ=255)
gTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCt < 1:3721190/38‑1 (MQ=255)
ttCGGGCGCGGTGACTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACCGGTTTGTTAt > 1:2145734/1‑67 (MQ=255)
tCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGc > 1:2263657/1‑52 (MQ=255)
cGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCtttt < 1:1533239/44‑1 (MQ=255)
gggCGCGGTGACTGCACTGTTACGGCTTTGGCTTCCTGCtttt < 1:1700896/43‑1 (MQ=38)
gTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACCGGttt < 1:1505071/52‑1 (MQ=255)
tGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACCGGtt < 1:2701392/50‑1 (MQ=255)
tGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACCGGTTTGTTATCCGCGCACGGCAAAt < 1:270557/71‑1 (MQ=255)
ggCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGt > 1:2590312/1‑39 (MQ=255)
gCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCg > 1:3516956/1‑36 (MQ=255)
gCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACCGGTTTGTTATCCGCGCAc < 1:771769/62‑1 (MQ=255)
gCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACCGGTTTGTTATCCGCGCACGGCAAATc < 1:3496969/70‑1 (MQ=255)
|
TATCGCCCTTCACTTTCTCGAAAGAAGGCAGCAACACGTAGGTTTTTTCCCACGGTTTCGGGCGCGGTGGCTGCACGGTTACGGCTTTGGCTTCCTGCTTTTTCGGTGCCACCGGTTTGTTATCCGCGCACGGCAAATC > minE/2022997‑2023135
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
