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 F28 I2 R2
|
356 |
55.1 |
4139924 |
95.4% |
3949487 |
63.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,396,058 |
A→G |
Y373C (TAT→TGT) |
mppA → |
murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,396,058 | 0 | A | G | 77.1%
| 93.9
/ 26.1
| 48 | Y373C (TAT→TGT) | mppA | murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit |
| Reads supporting (aligned to +/- strand): ref base A (6/5); new base G (16/21); total (22/26) |
| Fisher's exact test for biased strand distribution p-value = 7.32e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-01 |
GTTTGAACAAATGAGTCAGGAAGAACTGAATGCGCAGGCAAAAACTTTGTTGAGCGCAGCTGGTTATGGTCCGCAAAAACCGCTGAAGCTGACGCTTTTGTATAACACTTCAGAAAACCATCAAAA > W3110S.gb/1395993‑1396118
|
gTTTGAACAAATGAGTCAGGAAGAACTGAATGCGCAGGCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTc > 1:2099294/1‑71 (MQ=255)
gTTTGAACAAATGAGTCAGGAAGAACTGAATGCGCAGGCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTc > 1:718240/1‑71 (MQ=255)
gTTTGAACAAATGAGTCAGGAAGAACTGAATGCGCAGGCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTc > 1:1734097/1‑71 (MQ=255)
gTTTGAACAAATGAGTCAGGAAGAACTGAATGCGCAGGCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTc > 1:3816750/1‑71 (MQ=255)
gTTTGAACAAATGAGTCAGGAAGAACTGAATGCGCAGGCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTc > 1:1604310/1‑71 (MQ=255)
gTTTGAACAAATGAGTCAGGAAGAACTGAATGCGCAGGCAAAAACTTTGTTGACCGCAGCTGGTTGTGGTc > 1:1976619/1‑71 (MQ=255)
tGAACAAATGAGTCAGGAAGAACTGAATGCGCAGGCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCg > 1:3393314/1‑70 (MQ=255)
aGGAAGAACTGAATGCGCAGGCAAAAACTTTGTTGAGCGCAGCTGGTTATGGTCCGCAAAAACCGCTGAAg > 1:2108517/1‑71 (MQ=255)
aGGAAGAACTGAATGCGCAGGCAAAAACTTTGTTGAGCGCAGCTGGTTATGGTCCGCAAAAACCGCTGAAg > 1:74264/1‑71 (MQ=255)
aGGAAGAACTGAATGCGCAGGCAAAAACTTTGTTGAGCGCAGCTGGTTATGGTCCGCAAAAACCGCTGAAg > 1:2932779/1‑71 (MQ=255)
aaTGCGCAGGCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCTGACGCttt < 1:981004/70‑1 (MQ=255)
aaTGCGCAGGCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCTGACGCttt < 1:1877414/70‑1 (MQ=255)
aTGCGCAGGCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCTGACGCTTTTg < 1:3969660/71‑1 (MQ=255)
aTGCGCAGGCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCTGACGCTTTTg < 1:931740/71‑1 (MQ=255)
tGCGCAGGCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAg > 1:298513/1‑58 (MQ=255)
tGCGCAGGCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCt > 1:630609/1‑60 (MQ=255)
tGCGCAGGCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCt > 1:841989/1‑60 (MQ=255)
tGCGCAGGCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCt > 1:2649896/1‑60 (MQ=255)
tGCGCAGGCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCt > 1:1167432/1‑60 (MQ=255)
tGCGCAGGCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCt > 1:2487995/1‑60 (MQ=255)
tGCGCAGGCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCTGACGCTTTTg > 1:1130525/1‑70 (MQ=255)
tGCGCAGGCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCTGACGCTTTTg > 1:1198403/1‑70 (MQ=255)
cAGGCAAAAACTTTGTTGAGCGCAGCTGGTTATGGTCCGCAAAAACCGCTGAAGCTGACGCTTTTGTATaa < 1:2449816/71‑1 (MQ=255)
cAGGCAAAAACTTTGTTGAGCGCAGCTGGTTATGGTCCGCAAAAACCGCTGAAGCTGACGCTTTTGTATaa < 1:1407598/71‑1 (MQ=255)
cAGGCAAAAACTTTGTTGAGCGCAGCTGGTTATGGTCCGCAAAAACCGCTGAAGCTGACGCTTTTGTATaa < 1:1639622/71‑1 (MQ=255)
aGGCAAAAACTTTGTTGAGCGCAGCTGGTTATGGTCCGCAAAAACCGCTGAAGCTGACGCTTTTGTATaa < 1:1940219/70‑1 (MQ=255)
aGGCAAAAACTTTGTTGAGCGCAGCTGGTTATGGTCCGCAAAAACCGCTGAAGCTGACGCTTTTGTATaa < 1:1210932/70‑1 (MQ=255)
ggCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCTGACGc < 1:1035677/59‑1 (MQ=255)
ggCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCTGACGc < 1:2187669/59‑1 (MQ=255)
ggCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCTGACGc < 1:1155696/59‑1 (MQ=255)
ggCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCTGACGc < 1:1187946/59‑1 (MQ=255)
ggCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCTGACGc < 1:435644/59‑1 (MQ=255)
ggCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCTGACGc < 1:4046857/59‑1 (MQ=255)
ggCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCTGACGc < 1:3234613/59‑1 (MQ=255)
ggCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCTGACGc < 1:3140785/59‑1 (MQ=255)
ggCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCTGACGc < 1:2173494/59‑1 (MQ=255)
ggCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCTGACGCTTTTGTATAaca < 1:1263647/71‑1 (MQ=255)
ggCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGGCCGCAAAAACCGCTGAAGCTGACGc < 1:2675630/59‑1 (MQ=255)
gCAAAAACTTTGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCTGACGc < 1:1839198/58‑1 (MQ=255)
tttGTTGAGCGCAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCTGACGCTTTTGTATAACACTTCAGaa > 1:1871102/1‑70 (MQ=255)
gAGCGCAGCTGGTTATGGTCCGCAAAAACCGCTGAAGCTGACGCTTTTGTATAACACTTCAGAAAAc > 1:4050885/1‑67 (MQ=255)
gAGCGCAGCTGGTTATGGTCCGCAAAAACCGCTGAAGCTGACGCTTTTGTATAACACTTCAGAAAAc > 1:2853593/1‑67 (MQ=255)
gAGCGCAGCTGGTTATGGTCCGCAAAAACCGCTGAAGCTGACGCTTTTGTATAACACTTCAGAAAAc > 1:2278427/1‑67 (MQ=255)
gcAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCTGACGCTTTTGTATAACACTTCAGAAAACCATCaaaa < 1:3675850/71‑1 (MQ=255)
gcAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCTGACGCTTTTGTATAACACTTCAGAAAACCATCaaaa < 1:3023649/71‑1 (MQ=255)
gcAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCTGACGCTTTTGTATAACACTTCAGAAAACCATCaaaa < 1:2204400/71‑1 (MQ=255)
cAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCTGACGCTTTTGTATAACACTTCAGAAAACCATCaaaa < 1:61237/70‑1 (MQ=255)
cAGCTGGTTGTGGTCCGCAAAAACCGCTGAAGCTGACGCTTTTGTATAACACTTCAGAAAACCATCaaaa < 1:1200297/70‑1 (MQ=255)
|
GTTTGAACAAATGAGTCAGGAAGAACTGAATGCGCAGGCAAAAACTTTGTTGAGCGCAGCTGGTTATGGTCCGCAAAAACCGCTGAAGCTGACGCTTTTGTATAACACTTCAGAAAACCATCAAAA > W3110S.gb/1395993‑1396118
|
| 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
