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 |
|
A7 F123 I0 R1
|
30 |
27.0 |
575273 |
98.7% |
567794 |
141.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
1,776,114 |
G→A |
36.3% |
P137L (CCA→CTA) |
clpX ← |
ATP‑dependent Clp protease ATP‑binding subunit ClpX |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 1,776,114 | 0 | G | A | 36.3%
| 9.3
/ 16.8
| 21 | P137L (CCA→CTA) | clpX | ATP‑dependent Clp protease ATP‑binding subunit ClpX |
| Reads supporting (aligned to +/- strand): ref base G (4/8); new base A (3/4); total (7/14) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.80e-01 |
CTACATAAATAATACCTTTTTCGGCTTTATCAATGTCAAAGTCAGCTGCTTGAATTAATCTCAACAAGATATTTTCAACATCATCGCCTACATAACCAGCTTCAGTTAAACTTGTCGCATCTGCAATTGCAAATGGTACATTCAACGTCTTGGCTAAGGTTTGAGCTAATAATGTTTTACCACTACCTGTTGGCCCAATTAATGCAATGTTACTTTTTTGTAATTCAACATCATCTTCTTTTGGTCCTAATTGTTGAATACGCTTATAGT > USA300TCH1516_ALE/1775980‑1776249
|
cTACATAAATAATACCTTTTTCGGCTTTATCAATGTCAAAGTCAGCTGCTTGAATTAATCTCAACAAGATATTTTCAACATCATCGCCTACATAACCAGCTTCAGTTAAACTTGTCGCATCTGCAATTGCAAATAGTACAt < 1:77252/141‑1 (MQ=255)
aCATAAATAATACCTTTTTCGGCTTTATCAATGTCAAAGTCAGCTGCTTGAATTAATCTCAACAAGATATTTTCAACATCATCGCCTACATAACCAGCTTCAGTTAAACTTGTCGCATCTGCAATTGCAAATAGTACATTc < 1:564113/141‑1 (MQ=255)
cATAAATAATACCTTTTTCGGCTGTATCAATGTCAAAGTCAGCTGCTTGAATTAATCTCAACAAGATATTTTCAACATCATCGCCTACATAACCAGCTTCAGTTAAACTTGTCGCATCTGCAATTGCAAATAGTACATTCa < 1:93/141‑1 (MQ=255)
taCCTTTTTCGGCTTTATCAATGTCAAAGTCAGCTGCTTGAATTAATCTCAACAAGATATTTTCAACATCATCGCCTACATAACCAGCTTCAGTTAAACTTGTCGCATCTGCAATTGCAAATGGTACATTCAACGTCTTgg < 1:29623/141‑1 (MQ=255)
ttttCGGCTTTATCAATGTCAAAGTCAGCTGCTTGAATTAATCTCAACAAGATATTTTCAACATCATCGCCTACATAACCAGCTTCAGTTAAACTTGTCGCATCTGCAATTGCAAATGGTACATTCAACGTCTTGGCTAAg > 1:260149/1‑141 (MQ=255)
tCGGCTTTATCAATGTCAAAGTCAGCTGCTTGAATTAATCTCAACAAGATATTTTCAACATCATCGCCTACATAACCAGCTTCAGTTAAACTTGTCGCATCTGCAATTGCAAATGGTACATTCAACGTCTTGGCTAAGGtt < 1:66179/141‑1 (MQ=255)
cAATGTCAAAGTCAGCTGCTTGAATTAATCTCAACAAGATATTTTCAACATCATCGCCTACATAACCAGCTTCAGTTAAACTTGTCGCATCTGCAATTGCAAATGGTACATTCAACGTCTTTGCTAAGGTTTGAGCtaata < 1:322195/141‑1 (MQ=255)
cAATGTCAAAGTCAGCTGCTTGAATTAATCTCAACAAGATATTTTCAACATCATCGCCTACATAACCAGCTTCAGTTAAACTTGTCGCATCTGCAATTGCAAATGGTACATTCAACGTCTTGGCTAAGGTTTGAGCtaata < 1:321946/141‑1 (MQ=255)
cAGCTGCTTGAATTAATCTCAACAAGATATTTTCAACATCATCGCCTACATAACCAGCTTCAGTTAAACTTGTCGCATCTGCAATTGCAAATGGTACATTCAACGTCTTGGCTAAGGTTTGAGCTAATAATGTTTTACCAc > 1:429808/1‑141 (MQ=255)
gctTGAATTAATCTCAACAAGATATTTTCAACATCATCGCCTACATAACCAGCTTCAGTTAAACTTGTCGCATCTGCAATTGCAAATAGTACATTCAACGTCTTGGCTAAGGTTTGAGCTAATAATGTTTTACCACTACCt > 1:212138/1‑141 (MQ=255)
tGAATTAATCTCAACAAGATATTTTCAACATCATCGCCTACATAACCAGCTTCAGTTAAACTTGTCGCATCTGCAATTGCAAATGGTACATTCAACGTCTTGGCTAAGGTTTGAGCTAATAATGTTTTACCACTACCTGtt > 1:358182/1‑141 (MQ=255)
gATATTTTCAACATCATCGCCTACATAACCAGCTTCAGTTAAACTTGTCGCATCTGCAATTGCAAATGGTACATTCAACGTCTTGGCTAAGGTTTGAGCTAATAATGTTTTACCACTACCTGTTGGCCCAATTAATGCAAt > 1:58523/1‑141 (MQ=255)
catcGCCTACATAACCAGCTTCAGTTAAACTTGTCGCATCTGCAATTGCAAATCGTATTATTAGCGTCTTGGCTAAGGTTTGAGCTAATAATGTTTTACCACTACCTGTTGGCCCAATTAATGCAATGTTACTTTTTTGTa < 1:418165/141‑1 (MQ=255)
cATAACCAGCTTCAGTTAAACTTGTCGCATCTGCAATTGCAAATAGTACATTCAACGTCTTGGCTAAGGTTTGAGCTAATAATGTTTTACCACTACCTGTTGGCCCAATTAATGCAATGTTACTTTTTTGTAATTCAAcat < 1:498667/141‑1 (MQ=255)
aGCTTCAGTTAAACTTGTCGCATCTGCAATTGCAAATGGTACATTCAACGTCTTGGCTAAGGTTTGAGCTAATAATGTTTTACCACTACCTGTTGGCCCAATTAATGCAATGTTACTTTTTTGTAATTCAACATCAtcttc < 1:497931/141‑1 (MQ=255)
gCTTCAGTTAAACTTGTCGCATCTGCAATTGCAAATGGTACATTCAACGTCTTGGCTAAGGTTTGAGCTAATAATGTTTTACCACTACCTGTTGGCCCAATTAATGCAATGTTACTTTTTTGTAATTCAACATCAtcttct < 1:14082/141‑1 (MQ=255)
aaaCTTTTCGCATCTGCAATTGCAAATGGTACATTCAACGTCTGGGCTAAGGTTTGAGCTAATAATGTTTTACCACTACCTGTTGGCCCAATTAATGCAATGTTACTTTTTTGTAATTCAACATCATCTTCTTTTGGTCCt < 1:197374/141‑1 (MQ=255)
aaaCTTGTCGCATCTGCAATGGCAAATGGTACATTCAACGTCTTGGCTAAGGTTTGAGCTAATAATGTTTTACCACTACCTGTTGGCCCAATTAATGCAATGTTACTTTTTTGTAATTCAACATCATCTTCTTTTGGTCCt < 1:439322/141‑1 (MQ=255)
cATCTGCAATTGCAAATAGTACATTCAACGTCTTGGCTAAGGTTTGAGCTAATAATGTTTTACCACTACCTGTTGGCCCAATTAATGCAATGTTACTTTTTTGTAATTCAACATCATCTTCTTTTGGTCCTAATTGTTGaa > 1:198339/1‑141 (MQ=255)
aTTGCAAATAGTACATTCAACGTCTTGGCTAAGGTTTGAGCTAATAATGTTTTACCACTACCTGTTGGCCCAATTAATGCAATGTTACTTTTTTGTAATTCAACATCATCTTCTTTTGGTCCTAATTGTTGACTACGCTta > 1:508470/1‑141 (MQ=255)
cAAATTGTACATTCAACGTCTTGGCTAAGGTTTGAGCTAATAATGTTTTACCACTACCTGTTGGCCCAATTAATGCAATGTTACTTTTTTGTAATTCAACATCATCTTCTTTTGGTCCTAATTGTTGAATACGCTTATAGt < 1:361840/141‑1 (MQ=255)
|
CTACATAAATAATACCTTTTTCGGCTTTATCAATGTCAAAGTCAGCTGCTTGAATTAATCTCAACAAGATATTTTCAACATCATCGCCTACATAACCAGCTTCAGTTAAACTTGTCGCATCTGCAATTGCAAATGGTACATTCAACGTCTTGGCTAAGGTTTGAGCTAATAATGTTTTACCACTACCTGTTGGCCCAATTAATGCAATGTTACTTTTTTGTAATTCAACATCATCTTCTTTTGGTCCTAATTGTTGAATACGCTTATAGT > USA300TCH1516_ALE/1775980‑1776249
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
