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 |
|
A0 F0 I1 R1
|
149 |
26.7 |
2337422 |
87.5% |
2045244 |
105.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
1,402,540 |
C→G |
G893A (GGC→GCC) |
h16_A1292 ← |
ATP‑dependent transcriptional regulator,MalT‑family |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 1,402,540 | 0 | C | G | 100.0%
| 24.2
/ NA
| 8 | G893A (GGC→GCC) | h16_A1292 | ATP‑dependent transcriptional regulator,MalT‑family |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base G (6/2); total (6/2) |
AGTGCCATTTCACCGTCTCCGGCGACAGGCCCAGGGTGCGCGCAATCTTCTTGTTGGGCAGGCCCTGGCCGAGCAGGCGCACGACATCGGCTTCGCGGTCGCTCAGTTCCTCGAGGCGCGCGTCGGCCCGGGCCGGGCTGCCGGCGGGCGCGGCAGCCGCGGCGGTGCCGCCCGCCGCGCCGGCTTGCGCGGC > AM260479/1402478‑1402670
|
aGTGCCATTTCACCGTCTCCGGCGACAGGCCCAGGGTGCGCGCAATCTTCTTGTTGGGCAGGGCCTGGCCGAGCAGGCGCACGACATCGGCTTCGCGGTCGCTCAGTTCCTCGAGGCGCGCGTCGGCccgggcc > 1:790633/1‑134 (MQ=255)
cATTTCACCGTCTCCGGCGACAGGCCCAGGGTGCGCGCAATCTTCTTGTTGGGCAGGGCCTGGCCGAGCAGGCGCACGACATCGGCTTCGCGGTCGCTCAGTTCCTCGAGGCGCGCGTCGGCCCGGGCCGGGCt > 1:454342/1‑134 (MQ=255)
gcgcAATCTTCTTGTTGGGCAGGGCCTGGCCGAGCAGGCGCACGACATCGGCTTCGCGGTCGCTCAGTTCCTCGAGGCGCGCGTCGGCCCGGGCCGGGCTGCCGGCGGGCGCGGCAGCCGCGGCGGTGccgccc > 1:1034958/1‑134 (MQ=255)
cAATCTTCTTGTTGGGCAGGGCCTGGCCGAGCAGGCGCACGACATCGGc < 1:607850/49‑1 (MQ=255)
cAATCTTCTTGTTGGGCAGGGCCTGGCCGAGCAGGCGCACGACATCGGc > 2:607850/1‑49 (MQ=255)
aTCTTCTTGTTGGGCAGGGCCTGGCCGAGCAGGCGCACGACATCGGCTTCGCGGTCGCTCAGTTCCTCGAGGCGCGCGTCGGCCCGGGCCGGGCTGCCGGCGGGCGCGGCAGCCGCGGCGGTGCCGCCcgccgc > 1:794589/1‑134 (MQ=255)
aGGGCCTGGCCGAGCAGGCGCACGACATCGGCTTCGCGGTCGCTCAGTTCCTCGAGGCGCGCGt < 2:95330/64‑1 (MQ=255)
aGGGCCTGGCCGAGCAGGCGCACGACATCGGCTTCGCGGTCGCTCAGTTCCTCGAGGCGCGCGTCGGCCCGGGCCGGGCTGCCGGCGGGCGCGGCAGCCGCGGCGGTGCCGCCCGCCGCGCCGGCTTgcgcggc > 1:432125/1‑134 (MQ=255)
|
AGTGCCATTTCACCGTCTCCGGCGACAGGCCCAGGGTGCGCGCAATCTTCTTGTTGGGCAGGCCCTGGCCGAGCAGGCGCACGACATCGGCTTCGCGGTCGCTCAGTTCCTCGAGGCGCGCGTCGGCCCGGGCCGGGCTGCCGGCGGGCGCGGCAGCCGCGGCGGTGCCGCCCGCCGCGCCGGCTTGCGCGGC > AM260479/1402478‑1402670
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GTCCAGCTCGCGGTCGCGGACGCGCGCCACGGCCTCGTCGCGGCTGCTCACGCCCAGCTTGCGGAAGATGTTGCGCAAGTGCCATTTCACCGTCTCCGGCGACAGGCCCAGGGTGCGCGCAATCTTCTTGTTGGGCAGGCCCTGGCCGAGCAGGCGCACGACATCGGCTTCGCGGTCGCTCAGTTCCTCGAGGCGCGCGTCGGCCCGGGCCGGGCTGCCGGCGGGCGCGGCAGCCGCGGCGGTGCCGCCCGCCGCGCCGGCTTGCGCGGCGCGCGGCGGCACGGTGGCC > AM260479/1402401‑1402689
|
ttttttttttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagGTGCCATTTCACCGTCTCCGGCGACAGGCCCAGGGTGCGCGCAATCTTCTTGTTGGGCAGGGCCTGGCC < GWNJ‑0478:712:GW2002102894th:2:2114:10581:80351/69‑1 (MQ=60)
ggtctggagcctggtgttaccagtgcctgcccttgtttttttttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagGGGCAGGGCCTGGCCGAGCAGGCGCACGACATCGGC < GWNJ‑0478:712:GW2002102894th:2:1114:12152:100665/36‑1 (MQ=60)
ttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagGGCCCAGGGTGCGCGCAATCTTCTTGTTGGGCAGGGCCTGGCCGAGCAGGCGCACGACATCGGCTTCGCGGTCGCTCAG < GWNJ‑0478:712:GW2002102894th:2:2102:20680:11974/79‑1 (MQ=60)
GGAAGATGTTGCGCAAGTGCCATTTCACCGTCTCCGGCGACAGGCCCAGGGTGCGCGCAATCTTCTTGTTGGGCAGGGCCTGGCCGAGCAGGCGCACGACATCGGCTTCGCGGTCGCTCAGTTCCTCGAGGCGCGCGTCGGCCCGGGCCG > GWNJ‑0478:712:GW2002102894th:2:2112:3155:29039/1‑150 (MQ=60)
ATGTTGCGCAAGTGCCATTTCACCGTCTCCGGCGACAGGCCCAGGGTGCGCGCAATCTTCTTGTTGGGCAGGGCCTGGCCGAGCAGGCGCACGACATCGGCTTCGCGGTCGCTCAGTTCCTCGAGGCGCGCGTCGGCCCGGGCCGGGCTG > GWNJ‑0478:712:GW2002102894th:2:1210:15873:16309/1‑150 (MQ=60)
ACAGGCCCAGGGTGCGCGCAATCTTCTTGTTGGGCAGGGCCTGGCCGAGCAGGCGCACGACATCGGCTTCGCGGTCGCTCAGTTCCTCGAGGCGCGCGTCGGCCCGGGCCGGGCTGCCGGCGGGCGCGGCAGCCGCGGCGGTGCCGCCCG > GWNJ‑0478:712:GW2002102894th:2:2211:5629:68925/1‑150 (MQ=60)
CCCAGGGTGCGCGCAATCTTCTTGTTGGGCAGGGCCTGGCCGAGCAGGCGCACGACATCGGCTTCGCGGTCGCTCAGTTCCTCGAGGCGCGCGTCGGCCCGGGCCGGGCTGCCGGCGGGCGCGGCAGCCGCGGCGGTGCCGCCCGCCGCG > GWNJ‑0478:712:GW2002102894th:2:2112:7587:48049/1‑150 (MQ=60)
ATCTTCTTGTTGGGCAGGGCCTGGCCGAGCAGGCGCACGACATCGGCctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaaacacagcgaacagcacagaacg > GWNJ‑0478:712:GW2002102894th:2:2109:16010:66267/1‑47 (MQ=60)
ATCTTCTTGTTGGGCAGGGCCTGGCCGAGCAGGCGCACGACATCGGCTTCGCGGTCGCTCAGTTCCTCGAGGCGCGCGTCGGCCCGGGCCGGGCctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgt > GWNJ‑0478:712:GW2002102894th:2:1107:10240:96414/1‑94 (MQ=60)
ATCTTCTTGTTGGGCAGGGCCTGGCCGAGCAGGCGCACGACATCGGCTTCGCGGTCGCTCAGTTCCTCGAGGCGCGCGTCGGCCCGGGCCGGGCTGCCGGCGGGCGCGGCAGCCGCGGCGGTGCCGCCCGCCGCGCCGGCTTGCGCGGCG > GWNJ‑0478:712:GW2002102894th:2:1209:13042:99056/1‑150 (MQ=60)
GCCTGGCCGAGCAGGCGCACGACATCGGCTTCGCGGTCGCTCAGTTCCTCGAGGCGCGCGTCGGCCCGGGCCGGGCTGCCGGCGGGCGCGGCgggcggcggcacggtggcctgcaggcgttcgacatagactgtctcttatacacatctc > GWNJ‑0478:712:GW2002102894th:2:1205:17286:6689/1‑92 (MQ=60)
|
GTCCAGCTCGCGGTCGCGGACGCGCGCCACGGCCTCGTCGCGGCTGCTCACGCCCAGCTTGCGGAAGATGTTGCGCAAGTGCCATTTCACCGTCTCCGGCGACAGGCCCAGGGTGCGCGCAATCTTCTTGTTGGGCAGGCCCTGGCCGAGCAGGCGCACGACATCGGCTTCGCGGTCGCTCAGTTCCTCGAGGCGCGCGTCGGCCCGGGCCGGGCTGCCGGCGGGCGCGGCAGCCGCGGCGGTGCCGCCCGCCGCGCCGGCTTGCGCGGCGCGCGGCGGCACGGTGGCC > AM260479/1402401‑1402689
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
