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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,489,703 |
C→G |
26.6% |
S234S (TCC→TCG) |
dnaN → |
DNA polymerase III, beta subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,489,703 | 0 | C | G | 26.6%
| 64.7
/ 21.8
| 45 | S234S (TCC→TCG) | dnaN | DNA polymerase III, beta subunit |
| Reads supporting (aligned to +/- strand): ref base C (26/7); new base G (6/6); total (32/13) |
| Fisher's exact test for biased strand distribution p-value = 7.57e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.75e-01 |
CCGCTGCGCGTACAGATTGGCAGCAACAACATTCGCGCCCACGTTGGCGACTTTATCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCGGATTATCGCCGCGTTCTGCCGAAGAACCCGGACAAACATC > minE/2489638‑2489767
|
ccGCTGCGCGTACAGATTGGCAGCAACAACATTCGCGCCCACGTTGGCGACTTTATCTTCACCTCCaaa > 1:2533158/1‑69 (MQ=255)
ccGCTGCGCGTACAGATTGGCAGCAACAACATTCGCGCCCACGTTGGCGACTTTATCTTCACCTCCaaa > 1:3119777/1‑69 (MQ=255)
gCTGCGCGTGCAGATTGGCAGCAACAACATTCGCGCCCACGTTGGCGACTTTATCTTCACCTCGAAAc > 1:1910857/1‑68 (MQ=255)
gCTGCGCGTGCAGATTGGCAGCAACAACATTCGCGCCCACGTTGGCGACTTTATCTTCACCTCGAAAc > 1:1919422/1‑68 (MQ=255)
gCTGCGCGTGCAGATTGGCAGCAACAACATTCGCGCCCACGTTGGCGACTTTATCTTCACCTCGAAACt > 1:2315356/1‑69 (MQ=255)
gCTGCGCGTGCAGATTGGCAGCAACAACATTCGCGCCCACGTTGGCGACTTTATCTTCACCTCGAAACt > 1:487520/1‑69 (MQ=255)
gCTGCGCGTGCAGATTGGCAGCAACAACATTCGCGCCCACGTTGGCGACTTTATCTTCACCTCGAAACt > 1:3114784/1‑69 (MQ=255)
gCTGCGCGTGCAGATTGGCAGCAACAACATTCGCGCCCACGTTGGCGACTTTATCTTCACCTCGAAACt > 1:386519/1‑69 (MQ=255)
tGCGCGTGCAGATTGGCAGCAACAACATTCGCGCCCACGTTGGCGACTTTATCTTCACCTCGAAACtgg < 1:1599602/69‑1 (MQ=255)
tGCGCGTGCAGATTGGCAGCAACAACATTCGCGCCCACGTTGGCGACTTTATCTTCACCTCGAAACtgg < 1:2057545/69‑1 (MQ=255)
tGCGCGTGCAGATTGGCAGCAACAACATTCGCGCCCACGTTGGCGACTTTATCTTCACCTCGAAACtgg < 1:3157873/69‑1 (MQ=255)
tGCGCGTGCAGATTGGCAGCAACAACATTCGCGCCCACGTTGGCGACTTTATCTTCACCTCGAAACtgg < 1:3098715/69‑1 (MQ=255)
gcgcGTGCAGATTGGCAGCAACAACATTCGCGCCCACGTTGGCGACTTTATCTTCACCTCGAAACtgg < 1:2234021/68‑1 (MQ=255)
acaacaTTCGCGCCCACGTTGGCGACTTTATCTTCACCTCGAAACtgg < 1:1363656/48‑1 (MQ=255)
aacaTTCGCGCCCACGTTGGCGACTTTATCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCGGATTAt > 1:1371542/1‑69 (MQ=255)
aacaTTCGCGCCCACGTTGGCGACTTTATCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCGGATTAt > 1:1915529/1‑69 (MQ=255)
aacaTTCGCGCCCACGTTGGCGACTTTATCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCGGATTAt > 1:2148251/1‑69 (MQ=255)
cgcgCCCACGTTGGCGACTTTATCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCg > 1:2876741/1‑57 (MQ=255)
cgcgCCCACGTTGGCGACTTTATCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCg > 1:482303/1‑57 (MQ=255)
cgcgCCCACGTTGGCGACTTTATCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCg > 1:762657/1‑57 (MQ=255)
cgcgCCCACGTTGGCGACTTTATCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCGGATTATcgccgc > 1:1543351/1‑69 (MQ=255)
cgcgCCCACGTTGGCGACTTTATCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCGGATTATcgccgc > 1:2325158/1‑69 (MQ=255)
cgcgCCCACGTTGGCGACTTTATCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCGGATTATcgccgc > 1:2988931/1‑69 (MQ=255)
cgcgCCCACGTTGGCGACTTTATCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCGGATTATcgccgc > 1:946363/1‑69 (MQ=255)
cgcgCCCACGTAGGCGACTTTATCTTCACCTCCaa > 1:2477124/1‑35 (MQ=255)
ggCGACTTTATCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCg > 1:1051656/1‑45 (MQ=255)
ggCGACTTTATCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCGGATTATCGCCGCGTTCTGCCgaag > 1:3052631/1‑69 (MQ=255)
ggCGACTTTATCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCGGATTATCGCCGCGTTCTGCCgaag > 1:853053/1‑69 (MQ=255)
ggCGACTTTATCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCGGATTATCGCCGCGTTCTGCCgaag > 1:1673945/1‑69 (MQ=255)
ggCGACTTTATCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCGGATTATCGCCGCGTTCTGCCgaag > 1:440666/1‑69 (MQ=255)
ggCGACTTTATCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCGGAATATcgc > 1:2188388/1‑54 (MQ=255)
tATCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCGGATTATCGCCGCGTTCTGCCGAAGAACCCgg > 1:2179300/1‑68 (MQ=255)
tATCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCGGATTATCGCCGCGTTCTGCCGAAGAACCCgg > 1:346152/1‑68 (MQ=255)
aTCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCGGATTATCGCCGCGTTCTGCCTAAGAACCCGGa > 1:1998384/1‑68 (MQ=255)
aTCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCGGATTATCGCCGCGTTCTGCCGAAGAACCCGGa > 1:2909612/1‑68 (MQ=255)
aTCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCGGATTATCGCCGCGTTCTGCCGAAGAACCCGGa > 1:935356/1‑68 (MQ=255)
aTCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCGGATTATCGCCGCGTTCTGCCGAAGAACCCGGa > 1:3206577/1‑68 (MQ=255)
aTCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCGGATTATCGCCGCGTTCTGCCGAAGAACCCGGa > 1:2444721/1‑68 (MQ=255)
tCCAAACTGGTGGATGGTCGCTTCCCGGATTATCGCCGCGTTCTGCCGAAGAACCCGGACAAACATc < 1:2307380/67‑1 (MQ=255)
tCCAAACTGGTGGATGGTCGCTTCCCGGATTATCGCCGCGTTCTGCCGAAGAACCCGGACAAACATc < 1:1701820/67‑1 (MQ=255)
tCCAAACTGGTGGATGGTCGCTTCCCGGATTATCGCCGCGTTCTGCCGAAGAACCCGGACAAACATc < 1:1324137/67‑1 (MQ=255)
tCCAAACTGGTGGATGGTCGCTTCCCGGATTATCGCCGCGTTCTGCCGAAGAACCCGGACAAACATc < 1:814059/67‑1 (MQ=255)
tCCAAACTGGTGGATGGTCGCTTCCCGGATTATCGCCGCGTTCTGCCGAAGAACCCGGACAAACATc < 1:308392/67‑1 (MQ=255)
tCCAAACTGGTGGATGGTCGCTTCCCGGATTATCGCCGCGTTCTGCCGAAGAACCCGGACAAACATc < 1:2737662/67‑1 (MQ=255)
tCCAAACTGGTGGATGGTCGCTTCCCGGATTATCGCCGCGTTCTGCCGAAGAACCCGGACAAACATc < 1:1191271/67‑1 (MQ=255)
|
CCGCTGCGCGTACAGATTGGCAGCAACAACATTCGCGCCCACGTTGGCGACTTTATCTTCACCTCCAAACTGGTGGATGGTCGCTTCCCGGATTATCGCCGCGTTCTGCCGAAGAACCCGGACAAACATC > minE/2489638‑2489767
|
| 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
