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 |
2,137,703 |
C→T |
44.7% |
P56P (CCG→CCA) |
truB ← |
tRNA pseudouridine synthase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,137,703 | 0 | C | T | 44.7%
| 6.8
/ 35.8
| 47 | P56P (CCG→CCA) | truB | tRNA pseudouridine synthase |
| Reads supporting (aligned to +/- strand): ref base C (9/17); new base T (10/11); total (19/28) |
| Fisher's exact test for biased strand distribution p-value = 3.90e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.72e-01 |
GACCCGATAGCGTTTGTCGGAGTCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATCGGCAACATGCCGGTCGCCAGCGGGTCCAGCGCACCGGTATGCCCGGCACGGTTGGCGTTATATATAC > minE/2137637‑2137770
|
gACCCGATAGCGTTTGTCGGAGTCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATCg > 1:723550/1‑68 (MQ=255)
cGGAGTCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATTGGCAACa > 1:2933594/1‑57 (MQ=255)
cGGAGTCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATTGGCAACATGCCGGTCGcc > 1:1202689/1‑68 (MQ=255)
cGGAGTCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATTGGCAACATGCCGGTCGcc > 1:2427154/1‑68 (MQ=255)
cGGAGTCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATTGGCAACATGCCGGTCGCCa > 1:248700/1‑69 (MQ=255)
cGGAGTCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATTGGCAACATGCCGGTCGCCa > 1:2774644/1‑69 (MQ=255)
cGGAGTCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATTGGCAACATGCCGGTCGCCa > 1:2241759/1‑69 (MQ=255)
cGGAGTCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATTGGCAACATGCCGGTCGCCa > 1:3076827/1‑69 (MQ=255)
cGGAGTCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATTGGCAACATGCCGGTCGCCa > 1:3103088/1‑69 (MQ=255)
cGGAGTCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATTGGCAACATGCCGGTCGCCa > 1:1631699/1‑69 (MQ=255)
cGGAGTCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATTGGCAACATGCCGGTCGCCa > 1:1437143/1‑69 (MQ=255)
ggAGTCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATCGGCAACATGCCGGTCGCCAg > 1:3242077/1‑69 (MQ=255)
ggAGTCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATCGGCAACATGCCGGTCGCCAg > 1:1532233/1‑69 (MQ=255)
aGTCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATCGGCAACATGCCGGTCGCCAGc < 1:1892235/68‑1 (MQ=255)
aGTCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATCGGCAACATGCCGGTCGCCAGc < 1:2987336/68‑1 (MQ=255)
aGTCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATCGGCAACATGCCGGTCGCCAGc < 1:2213530/68‑1 (MQ=255)
aGTCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATCGGCAACATGCCGGTCGCCAGc < 1:2263035/68‑1 (MQ=255)
tCCAGCAGATACTTGGAAAACTTCGTCGCTTCCCCGAGGCAAATTGGCAACATGCCGGTCGCCAGCggg < 1:403372/69‑1 (MQ=255)
tCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATTGGCAACATGCCGGTCGCCAGCggg < 1:2934147/69‑1 (MQ=255)
tCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATTGGCAACATGCCGGTCGCCAGCggg < 1:2904399/69‑1 (MQ=255)
tCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATTGGCAACATGCCGGTCGCCAGCggg < 1:2651428/69‑1 (MQ=255)
tCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATTGGCAACATGCCGGTCGCCAGCggg < 1:811803/69‑1 (MQ=255)
tCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATTGGCAACATGCCGGTCGCCAGCggg < 1:2457239/69‑1 (MQ=255)
tCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATTGGCAACATGCCGGTCGCCAGCggg < 1:2406011/69‑1 (MQ=255)
tCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATTGGCAACATGCCGGTCGCCAGCggg < 1:2385312/69‑1 (MQ=255)
tCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATTGGCAACATGCCGGTCGCCAGCggg < 1:2070335/69‑1 (MQ=255)
tCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATTGGCAACATGCCGGTCGCCAGCggg < 1:2038172/69‑1 (MQ=255)
tCCAGCAGATACTGGGAAAACTTCGTCCCTTCCCCGAGGCAAATTGGCAACATGCCGGTCGCCAGCggg < 1:1261053/69‑1 (MQ=255)
cagcagATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATCGGCAACATGCCGGTCGCCAGCggg > 1:2630768/1‑67 (MQ=255)
cagcagATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATCGGCAACATGCCGGTCGCCAGCggg > 1:1582432/1‑67 (MQ=255)
cagcagATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATCGGCAACATGCCGGTCGCCAGCggg > 1:1647377/1‑67 (MQ=255)
cgCTTCCCCGAGGCAAATCGGCAACATGCCGGTCGCCAGCGGGTCCAGCGCACCGGTATGCCCGGCAc < 1:2378498/68‑1 (MQ=255)
cgCTTCCCCGAGGCAAATCGGCAACATGCCGGTCGCCAGCGGGTCCAGCGCACCGGTATGCCCGGCAc < 1:3250483/68‑1 (MQ=255)
cgCTTCCCCGAGGCAAATCGGCAACATGCCGGTCGCCAGCGGGTCCAGCGCACCGGTATGCCCGGCAc < 1:339455/68‑1 (MQ=255)
cgCTTCCCCGAGGCAAATCGGCAACATGCCGGTCGCCAGCGGGTCCAGCGCACCGGTATGCCCGGCAc < 1:1453531/68‑1 (MQ=255)
gCTTCCCCGAGGCAAATCGGCAACATGCCGGTCGCCAGCGGGTCCAGCGCACCGGTATGCCCGGCACgg < 1:3059640/69‑1 (MQ=255)
gCTTCCCCGAGGCAAATCGGCAACATGCCGGTCGCCAGCGGGTCCAGCGCACCGGTATGCCCGGCACgg < 1:1713437/69‑1 (MQ=255)
gCTTCCCCGAGGCAAATCGGCAACATGCCGGTCGCCAGCGGGTCCAGCGCACCGGTATGCCCGGCACgg < 1:3427330/69‑1 (MQ=255)
gCTTCCCCGAGGCAAATCGGCAACATGCCGGTCGCCAGCGGGTCCAGCGCACCGGTATGCCCGGCACgg < 1:3430996/69‑1 (MQ=255)
gCTTCCCCGAGGCAAATCGGCAACATGCCGGTCGCCAGCGGGTCCAGCGCACCGGTATGCCCGGCACgg < 1:453644/69‑1 (MQ=255)
gCTTCCCCGAGGCAAATCGGCAACATGCCGGTCGCCAGCGGGTCCAGCGCACCGGTATGCCCGGCACgg < 1:564121/69‑1 (MQ=255)
gCTTCCCCGAGGCAAATCGGCAACATGCCGGTCGCCAGCGGGTCCAGCGCACCGGTATGCCCGGCACgg < 1:1022951/69‑1 (MQ=255)
gCAAATCGGCAACATGCCGGTCGCCAGCGGGTCCAGCGCACCGGTATGCCCGGCACGGTTGGCGTtata < 1:3154104/69‑1 (MQ=255)
gCAAATCGGCAACATGCCGGTCGCCAGCGGGTCCAGCGCACCGGTATGCCAGGCACGGTTGGCGTtata < 1:348860/69‑1 (MQ=255)
tCGGCAACATGCCGGTCGCCAGCGGGTCCAGCGCACCGGTATGCCCGGCACg > 1:1969315/1‑52 (MQ=255)
tCGGCAACATGCCGGTCGCCAGCGGGTCCAGCGCACCGGTATGCCCGGCACGGTTGGCGTTATATATAc > 1:3027746/1‑69 (MQ=255)
tCGGCAACATGCCGGTCGCCAGCGGGTCCAGCGCACCGGTATGCCCGGCACGGTTGGCGTTATATATAc > 1:2816559/1‑69 (MQ=255)
|
GACCCGATAGCGTTTGTCGGAGTCCAGCAGATACTGGGAAAACTTCGTCGCTTCCCCGAGGCAAATCGGCAACATGCCGGTCGCCAGCGGGTCCAGCGCACCGGTATGCCCGGCACGGTTGGCGTTATATATAC > minE/2137637‑2137770
|
| 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
