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 |
|
A3 F1 I2 R1
|
777 |
59.2 |
2955938 |
92.5% |
2734242 |
106.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,995,231 |
(A)7→8 |
intergenic (‑139/+83) |
ygeK ← / ← ygeN |
pseudogene, response regulator family, part of T3SS PAI ETT2 remnant, putative 2‑component transcriptional regulator/pseudogene, orgB family, part of T3SS PAI ETT2 remnant |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,995,224 | 1 | . | A | 87.5%
| 41.3
/ ‑0.2
| 16 | intergenic (‑132/+90) | ygeK/ygeN | pseudogene, response regulator family, part of T3SS PAI ETT2 remnant, putative 2‑component transcriptional regulator/pseudogene, orgB family, part of T3SS PAI ETT2 remnant |
| Reads supporting (aligned to +/- strand): ref base . (1/1); new base A (8/6); total (9/7) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATT‑AAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGG > NC_000913/2995104‑2995329
|
gAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATT‑AAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGc > 2:414125/1‑139 (MQ=255)
gAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATT‑AAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGc > 2:723692/1‑139 (MQ=255)
aaaaTGTTTTAACGCATTAATTAATATCAATCCTTTCAATAATAATAAAAAGCAAAATCCAAAAATAACTTTGA‑GAAATTAAAAAGAAAAATAATTAAAAAATAAAATTTTTCGGA‑AAAAAAATACCACAGGCATTaaa < 2:797418/138‑1 (MQ=255)
aaaTTCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATT‑AAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTaaa < 2:413802/139‑1 (MQ=255)
aaTGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATT‑AAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTaaaa > 1:292008/1‑139 (MQ=255)
ttAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATT‑AAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCAt > 1:898288/1‑139 (MQ=255)
ttAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATT‑AAAAATAAAATTTTTGCGT‑AAAAAAATAACAAAAGCAATaaaaaaataat > 1:797418/1‑134 (MQ=255)
aCGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATT‑AAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATgag < 1:414125/139‑1 (MQ=255)
cattTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATT‑AAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTa < 1:723692/139‑1 (MQ=255)
atcatcCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATT‑AAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTa < 1:364857/139‑1 (MQ=255)
atcCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATT‑AAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACaa < 1:1188708/139‑1 (MQ=255)
ttattatAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATT‑AAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTc > 1:1197084/1‑139 (MQ=255)
ataAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATT‑AAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAAta > 1:1146728/1‑138 (MQ=255)
ataAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATT‑AAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATc > 1:1462668/1‑139 (MQ=255)
aaaGAATACATTGATGAAATAATAATGAAATATAATT‑AAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGc > 2:789143/1‑139 (MQ=255)
aatGAAATATAATT‑AAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAggg < 1:789143/139‑1 (MQ=255)
|
GAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATT‑AAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGG > NC_000913/2995104‑2995329
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ 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
