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 |
|
A1 F3 I0 R1
|
560 |
56.4 |
4650532 |
94.9% |
4413354 |
59.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,824,326 |
T→C |
100% |
pseudogene (459/687 nt) |
rph → |
ECK3633:JW3618:b3643; ribonuclease PH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,824,326 | 0 | T | C | 100.0%
| 213.5
/ NA
| 63 | pseudogene (459/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (31/32); total (31/32) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TGCCTGCGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCT > W3110S.gb/3824263‑3824391
|
tGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa < 1:1189798/71‑1 (MQ=255)
tGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa < 1:3355073/71‑1 (MQ=255)
tGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa < 1:2228531/71‑1 (MQ=255)
cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGa > 1:1106436/1‑62 (MQ=255)
cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGa > 1:1422445/1‑71 (MQ=255)
cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGa > 1:238631/1‑71 (MQ=255)
tGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGAt < 1:1365718/70‑1 (MQ=255)
gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGa > 1:2023847/1‑58 (MQ=255)
cgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGt < 1:3602334/70‑1 (MQ=255)
tGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGcc > 1:2702474/1‑71 (MQ=255)
ggcaGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCg > 1:2860997/4‑71 (MQ=255)
ggcaGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGACGGTAg > 1:2463316/4‑68 (MQ=255)
aGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAg > 1:142883/1‑71 (MQ=255)
gATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATg < 1:1665398/51‑1 (MQ=255)
gATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATg < 1:562598/51‑1 (MQ=255)
gATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATg < 1:196986/51‑1 (MQ=255)
aTGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGa > 1:316008/1‑48 (MQ=255)
gcgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGa > 1:2271810/1‑46 (MQ=255)
gcgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGa > 1:439859/1‑46 (MQ=255)
gcgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa > 1:1021005/1‑51 (MQ=255)
gcgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTc > 1:107046/1‑71 (MQ=255)
gcgcTACAGAAGCTGGTGGAAAACGACAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGc > 1:3540280/1‑62 (MQ=39)
cgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTc < 1:4041581/70‑1 (MQ=255)
cgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCt < 1:1668961/71‑1 (MQ=255)
cTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa < 1:4018910/46‑1 (MQ=255)
cTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa < 1:989475/46‑1 (MQ=255)
cTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCt < 1:2972781/69‑1 (MQ=255)
tACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAAccc < 1:91175/40‑1 (MQ=255)
tACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGt < 1:1583793/70‑1 (MQ=255)
cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAg < 1:789793/46‑1 (MQ=255)
aGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGtt < 1:653812/62‑1 (MQ=255)
aGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg > 1:1863941/1‑70 (MQ=255)
gAAGCTGGTGGAAAACGGCAAGCT‑AAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt > 1:3541071/1‑71 (MQ=255)
aaGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATg > 1:2718226/1‑39 (MQ=255)
aGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGAt < 1:4370492/37‑1 (MQ=255)
gCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa > 1:526447/1‑40 (MQ=255)
gCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGt > 1:3000895/1‑57 (MQ=255)
gCTGGTGGAAAACGGCAAGCTAAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtg > 1:1882778/1‑71 (MQ=255)
cTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa < 1:4272870/37‑1 (MQ=255)
cTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCt < 1:3905519/60‑1 (MQ=255)
ggtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgta > 1:2182377/1‑69 (MQ=255)
gtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATTGTAGCCGCAGTTTCTGTCGGTATtgta < 1:4150086/69‑2 (MQ=255)
gtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgta < 1:4318499/69‑2 (MQ=255)
gtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgta < 1:2447553/69‑2 (MQ=255)
gtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCCGTATtgta < 1:627803/69‑2 (MQ=255)
tggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGa < 1:2140659/39‑1 (MQ=255)
tggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGa < 1:968488/39‑1 (MQ=255)
gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAAc > 1:995782/1‑69 (MQ=255)
gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACgg > 1:1337466/1‑71 (MQ=255)
aaaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGa > 1:4329514/1‑36 (MQ=255)
aaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCGGTTTCTGTCGGTATTGTAAACggtg > 1:1945324/1‑68 (MQ=255)
aaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGa < 1:2500796/71‑1 (MQ=255)
aaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTCCTGTCGGTATTGTAAACggt < 1:4133424/69‑2 (MQ=255)
cGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCggta < 1:1653725/56‑3 (MQ=255)
cAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaa < 1:2889462/71‑3 (MQ=255)
aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat > 1:3900787/1‑68 (MQ=255)
aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaa < 1:3291098/70‑3 (MQ=255)
aGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg < 1:3481207/63‑3 (MQ=255)
tGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGt > 1:275713/1‑43 (MQ=255)
gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc > 1:1521820/1‑70 (MQ=255)
aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAAc < 1:3833043/54‑1 (MQ=255)
aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt > 1:923239/1‑71 (MQ=255)
aaaCCAACCCGATGAAAGGGATGGTAG‑CGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc > 1:3602103/1‑71 (MQ=255)
aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat > 1:1767980/1‑60 (MQ=255)
aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca < 1:2633326/61‑2 (MQ=255)
aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCt > 1:655273/1‑71 (MQ=255)
|
TGCCTGCGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCT > W3110S.gb/3824263‑3824391
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
