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 F21 I0 R1
|
476 |
35.3 |
2812105 |
96.7% |
2719305 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,405,345 |
G→A |
17.8% |
intergenic (+67/‑9) |
hfq → / → hflX |
HF‑I, host factor for RNA phage Q beta replication/predicted GTPase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,405,345 | 0 | G | A | 17.8%
| 107.8
/ 15.1
| 45 | intergenic (+67/‑9) | hfq/hflX | HF‑I, host factor for RNA phage Q beta replication/predicted GTPase |
| Reads supporting (aligned to +/- strand): ref base G (20/17); new base A (6/2); total (26/19) |
| Fisher's exact test for biased strand distribution p-value = 4.35e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.96e-01 |
TAAGGTTTCGGGCTGTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTACACATCTATTTTAC > W3110S.gb/4405276‑4405409
|
tAAGGTTTCGGGCTGTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGt < 1:2375315/71‑1 (MQ=255)
tAAGGTTTCGGGCTGTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGt < 1:213260/71‑1 (MQ=255)
tAAGGTTTCGGGCTGTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGt < 1:1588800/71‑1 (MQ=255)
tCGGGCTGTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTtata > 1:2526421/1‑68 (MQ=255)
tCGGGCTGTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGc > 1:2491690/1‑71 (MQ=255)
gCTGTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTg < 1:325407/70‑1 (MQ=255)
tttttttACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTg < 1:450622/70‑1 (MQ=255)
ttttttACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGAc > 1:1190117/1‑71 (MQ=255)
ttACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGATTATACGCTTGTTTGACCGt < 1:620583/70‑1 (MQ=255)
cacGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTat < 1:2256770/70‑1 (MQ=255)
ggggAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGATTATACGCTTGTTTGACCGTTatgatg > 1:2352329/1‑71 (MQ=255)
gggAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGc < 1:1541894/71‑1 (MQ=255)
ggAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCt > 1:1562539/1‑71 (MQ=255)
ggAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCt < 1:2077922/71‑1 (MQ=255)
gAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGt < 1:1387571/42‑1 (MQ=255)
cAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGt > 1:700760/1‑69 (MQ=255)
aGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAg > 1:558504/1‑71 (MQ=255)
aTCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAgg > 1:399971/1‑71 (MQ=255)
ccTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTatga > 1:1486028/1‑55 (MQ=255)
ccTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCg > 1:156237/1‑71 (MQ=255)
cTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGAcc < 1:1937418/47‑1 (MQ=255)
cTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGtt < 1:2576743/50‑1 (MQ=255)
cTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCgg < 1:455245/71‑1 (MQ=255)
cTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCgg > 1:2000370/1‑71 (MQ=255)
cTGCGTTCCCCGCTGATCTATTTAGAGGATTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCgg < 1:2295361/71‑1 (MQ=255)
ttCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTg < 1:2384854/39‑1 (MQ=255)
ttCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTg < 1:1573759/39‑1 (MQ=255)
ttCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTat < 1:562963/47‑1 (MQ=255)
ccccGCTGATCTATTTAGAGGATTATACGCTTGTTTGACCGTTATGATGc > 1:1197342/1‑50 (MQ=255)
ccccGCTGATCTATTTAGAGGATTATACGCTTGTTTGACCGTTATGATGc > 1:59503/1‑50 (MQ=255)
ccccGCTGATCTATTTAGAGGATTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTgg > 1:575474/1‑70 (MQ=255)
cccGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTa < 1:987762/71‑1 (MQ=255)
gATCTATTTAGAGGGTTATACTCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTacac < 1:2121886/68‑1 (MQ=255)
cTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTACACATCTAt > 1:1839571/1‑71 (MQ=255)
cTATTTAGAGGATTATACGCGTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTACACATCTAt > 1:1893827/1‑71 (MQ=255)
tttAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAg > 1:2071613/1‑44 (MQ=255)
tttAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTACACATCTAttt > 1:2374204/1‑70 (MQ=255)
tAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTgg > 1:2391550/1‑38 (MQ=255)
tAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTgg > 1:1094250/1‑38 (MQ=255)
tAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGc > 1:1362618/1‑43 (MQ=255)
tAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTACACATCTATTTTAc > 1:1461353/1‑71 (MQ=255)
tAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTACACATCTATTTTAc > 1:2253083/1‑71 (MQ=255)
tAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTACACATCTATTTTAc > 1:712357/1‑71 (MQ=255)
tAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTCGTGAGCAGGCGGTACTCGTACACATCTATTTTAc > 1:1306303/1‑71 (MQ=255)
tAGAGGATTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTACACATCTATTTTAc > 1:1649306/1‑71 (MQ=255)
gggTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTaca > 1:243552/1‑55 (MQ=255)
gggTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTaca > 1:2300256/1‑55 (MQ=255)
|
TAAGGTTTCGGGCTGTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTACACATCTATTTTAC > W3110S.gb/4405276‑4405409
|
| 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
