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
|
58 |
36.1 |
1832140 |
90.7% |
1661750 |
105.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,073,282 |
G→A |
G582R (GGA→AGA) |
flu → |
CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,073,282 | 0 | G | A | 96.7%
| 96.8
/ ‑6.3
| 30 | G582R (GGA→AGA) | flu | CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| Reads supporting (aligned to +/- strand): ref base G (1/0); new base A (15/14); total (16/14) |
| 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 |
CCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGA > NC_000913/2073148‑2073416
|
cccTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACa > 1:768175/1‑139 (MQ=255)
aaGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGa > 2:685887/1‑132 (MQ=255)
cGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCAcc < 1:753178/139‑1 (MQ=255)
cTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCAc > 2:524915/1‑131 (MQ=255)
cTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCAc < 1:524915/131‑1 (MQ=255)
cGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCt > 2:509545/1‑139 (MQ=255)
ccTCCGGTGCCACCTGGTATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCt > 1:522451/1‑139 (MQ=255)
ccACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACa < 1:509545/139‑1 (MQ=255)
ggAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATgg < 2:768175/139‑1 (MQ=255)
ccccGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGAtt > 1:637188/1‑58 (MQ=255)
ccccGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGAtt < 2:637188/58‑1 (MQ=255)
ccccGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCAc < 1:294442/72‑1 (MQ=255)
ccccGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCAc > 2:294442/1‑72 (MQ=255)
ccACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCg > 1:51278/1‑64 (MQ=255)
ccACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCg < 2:51278/64‑1 (MQ=255)
ggtggtGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATgg < 2:249244/108‑1 (MQ=255)
ggtggtGGATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATgg > 1:249244/1‑108 (MQ=255)
ggtggATGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGca > 1:403781/1‑139 (MQ=255)
aTGACCTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGaa > 2:527859/1‑139 (MQ=255)
ccTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCAGCATCAGCCTGCGTGTa > 2:184959/1‑115 (MQ=255)
ccTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCt > 2:586797/1‑108 (MQ=255)
ccTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCgtg < 1:94199/113‑1 (MQ=255)
ccTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCgtg > 2:94199/1‑113 (MQ=255)
ccTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTa < 1:184959/115‑1 (MQ=255)
ccTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGca > 2:462499/1‑130 (MQ=255)
ccTCAGCCATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGca < 1:462499/130‑1 (MQ=255)
ccTCAGCCATGCCACACAGATTCATTTCACCTGCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCt < 1:586797/108‑1 (MQ=255)
ccATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATgg < 1:660803/90‑1 (MQ=255)
ccATGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATgg > 2:660803/1‑90 (MQ=255)
tGCCAGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGa < 2:403781/139‑1 (MQ=255)
|
CCCTGAAGCTGACCGGCAGCACTGTGCTGAACGGTGCCATTGACCCCACGAATGTCACTCTCGCCTCCGGTGCCACCTGGAATATCCCCGATAACGCCACGGTGCAGTCGGTGGTGGATGACCTCAGCCATGCCGGACAGATTCATTTCACCTCCACCCGCACAGGGAAGTTCGTACCGGCAACCCTGAAAGTGAAAAACCTGAACGGACAGAATGGCACCATCAGCCTGCGTGTACGCCCGGATATGGCACAGAACAATGCTGACAGA > NC_000913/2073148‑2073416
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
