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 |
|
A20 F53 I0 R4
|
206 |
63.7 |
2487030 |
95.4% |
2372626 |
127.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP006881 |
3,725,239 |
2 bp→AA |
100% |
intergenic (‑71/‑457) |
U712_19205 ← / → U712_19210 |
Uncharacterized protein ywcI/Minor extracellular protease vpr |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP006881 | 3,725,239 | 0 | G | A | 98.1%
| 78.7
/ ‑6.3
| 28 | intergenic (‑71/‑458) | U712_19205/U712_19210 | Uncharacterized protein ywcI/Minor extracellular protease vpr |
| Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (19/8); minor base C (1/0); total (20/8) |
| 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 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| * | CP006881 | 3,725,240 | 0 | G | A | 100.0%
| 84.9
/ NA
| 28 | intergenic (‑72/‑457) | U712_19205/U712_19210 | Uncharacterized protein ywcI/Minor extracellular protease vpr |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (20/8); total (20/8) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑C‑TTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAACTAGTTTTTAG > CP006881/3725110‑3725363
||
gTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGa < 7:178287/139‑1 (MQ=255)
ttCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCGGCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGGGTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAtg > 3:289871/1‑138 (MQ=255)
aGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCCGGCAGC‑CTTTTT‑A‑GCCGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAGTTCTTTTCTCg > 7:201611/1‑139 (MQ=255)
aGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGCCGGCCGATGTCTTTTCTCg > 8:141885/1‑139 (MQ=255)
tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGCCGGCCGATTTCTTTTATCGCAAACTAGCGGGTCTa > 4:65951/1‑139 (MQ=255)
tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAGTTCTTTTCTCGCAAACTAGCGGctc > 1:165876/1‑137 (MQ=255)
aGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGAGTCTTTTTGGCTGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGAAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa < 8:67399/139‑1 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCCGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGCGTTGATTTGTCGGCAACTAGCCGGGGTAGCaaaa > 1:132172/1‑138 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCCGC‑CGTTTT‑T‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCCAGAAAAGACGGCCGATTTCGTTTGTCGCAAACTTGCGGCTCTTGCaaaa > 3:18788/1‑138 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTACCGGCTCGAGCAAAAc > 8:83991/1‑139 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTAGCAAACTAGCGGCTCTAGCaaaa > 8:242659/1‑138 (MQ=255)
aaGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGACAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCGCTAGCAAAACt > 7:134659/1‑138 (MQ=255)
aaGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACt > 1:76065/1‑138 (MQ=255)
aaGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTATCGCAAACTAGCGGCTCTAGCAAAACt > 7:173887/1‑138 (MQ=255)
aGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTTGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGGCGCACCCCGCAAGAAAAGACGGCCGATTTATTTTGTAGCAACCAAGCGGCTGGAACAAAAcaaa > 6:3270/1‑136 (MQ=255)
aGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGCCGGCCGCTTTGTTTTCTCGCAAACGATCGGAGCTAGCaaaagtga > 6:103842/1‑135 (MQ=255)
ccAAAGGTTTCATACAAAAACACCCCACCGCTTCTTTTTGCCCGCCCCC‑T‑TTTT‑ACCCCGCCCGTTTACTCCGCCCCCCCCCCCAATAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt < 3:230315/138‑1 (MQ=255)
caaaccGTTCCATACAAAAACAGCCCACCGCTTCTTTTGGGCAGCCCCCTT‑TTTT‑A‑CCCCCCGGTTTCCTCCCCCGCACCCCCAAACAAACCACGGCCGATTTCTTTTCTCGAAAACTAGCGGCTCTAGCAAAACTCAt < 6:262056/134‑1 (MQ=255)
aaaCTTTTAATATAAAAAAATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCCGCCCTTTTTCTCAGCCGCAGCCCGAAATAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGa < 7:246969/139‑1 (MQ=255)
aaaCGTTTCATAAAAAAACATCCCTCCGCTTTTTTTTGGCTGGCAGC‑CTTTTT‑A‑GCCGCCGTTTTTGTCCGCCGCAGCCCGCAATAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGa < 3:145451/139‑1 (MQ=255)
ccGTTACAAACAAAAACACCCCTCCGCTTCTTTTTGCCCGCCCCC‑C‑TTTTAA‑CCCGCCCGTTTTCCCCCCCCCCCCCCCAAACAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct < 2:10077/138‑1 (MQ=255)
acttttAATACAAAAACATCCCACCGCTTCTTTTTGGCTCGCAGCGT‑TTTT‑A‑ACAGCCGGTTTTCTCAGCCCCCGCCCGCAAGAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct < 7:192021/136‑1 (MQ=255)
aCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATGTCTTTTCTCGCAAACGTCCGGCTCAAGCAAAACTCCTGAct > 3:56788/1‑139 (MQ=255)
aCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CATTTT‑A‑GCAGCCCGTTTTCTAAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTATTCTCGCAAACTAGCGGCTAAAGAAAAACACATGCct > 4:253740/1‑139 (MQ=255)
ttCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTATATTCTCGCAAACTAGCGGCTCTAGCAAAACTCAAGACTCAAt > 7:200463/1‑139 (MQ=255)
cccTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCATTTATCGCAAACAAGCCGCTCGAGCAAAACTCATTCATCTATTATAGACCGTggga > 5:189382/1‑136 (MQ=255)
cccGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAGTTCTTTTCTCGCAAACTAGCGGCGCGTGCAAAACGCATGACTCTATGCTAGTCCGTGGAAAGAGAATTCTTTTTCACAATATGAGTGAAAAAACCAAc > 5:97465/1‑139 (MQ=255)
cAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAAC‑AGTTTTTAg > 7:288240/1‑138 (MQ=255)
||
GTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑C‑TTTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAACTAGTTTTTAG > CP006881/3725110‑3725363
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
