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 I1 R1
|
748 |
32.0 |
1685426 |
92.6% |
1560704 |
103.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,712,518 |
(C)6→8 |
intergenic (+360/‑251) |
nth → / → dtpA |
DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,712,512 | 1 | . | C | 79.0%
| 46.9
/ 9.0
| 19 | intergenic (+354/‑257) | nth/dtpA | DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A |
| Reads supporting (aligned to +/- strand): ref base . (2/2); new base C (8/7); total (10/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.96e-01 |
| * | NC_000913 | 1,712,512 | 2 | . | C | 79.0%
| 47.8
/ 9.0
| 19 | intergenic (+354/‑257) | nth/dtpA | DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A |
| Reads supporting (aligned to +/- strand): ref base . (2/2); new base C (8/7); total (10/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.96e-01 |
GGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑‑CCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGA > NC_000913/1712380‑1712636
||
ggTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑‑cccccc < 2:578390/139‑1 (MQ=255)
aTTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGGGAAATAGCAGAACATATCTCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGGCGTTACGTTTTTTGAAAAATTTaa > 2:262340/1‑139 (MQ=255)
cacTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCt > 1:465044/1‑139 (MQ=255)
cacTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑‑CCCCCCcctctca > 1:272121/1‑89 (MQ=255)
cacTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑‑CCCCCCcctctca < 2:272121/92‑4 (MQ=255)
tGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGa > 1:50103/1‑139 (MQ=255)
cACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGGGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTccc < 1:423165/139‑1 (MQ=255)
aGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGTATGGTTGAATTCCCCGcc < 2:465044/139‑1 (MQ=255)
aGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGcc < 2:50103/139‑1 (MQ=255)
aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑‑CCCCCCcctct < 2:804876/52‑2 (MQ=255)
aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑‑CCCCCCcctct > 1:804876/1‑51 (MQ=255)
aaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGc > 1:371090/1‑134 (MQ=255)
aaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTGGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGc < 2:371090/134‑1 (MQ=255)
aCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAAc < 1:671412/94‑1 (MQ=255)
aCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAAc > 2:671412/1‑94 (MQ=255)
cGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTaa < 2:286966/122‑1 (MQ=255)
cGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTaa > 1:286966/1‑122 (MQ=255)
cGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGa > 2:179895/1‑139 (MQ=255)
ttAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTaa < 1:729751/67‑1 (MQ=255)
ttAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTaa > 2:729751/1‑67 (MQ=255)
||
GGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑‑CCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGA > NC_000913/1712380‑1712636
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
