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 |
|
A1 F2 I230 R1
|
226 |
18.8 |
1048726 |
96.7% |
1014118 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,363,696 |
T→C |
F16S (TTC→TCC) |
pspD → |
phage shock protein PspD |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,363,696 | 0 | T | C | 100.0%
| 29.6
/ NA
| 11 | F16S (TTC→TCC) | pspD | phage shock protein PspD |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (4/7); total (4/7) |
TAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGG > NZ_CP009273/1363620‑1363746
|
tAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGc < 1:94242/90‑1 (MQ=255)
ccGTTTCCGTCAACTGTGAGGAAAGTTATGAATTCTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAg < 2:273547/90‑1 (MQ=255)
gTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCt > 1:186992/1‑90 (MQ=255)
gTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCt < 1:452268/90‑1 (MQ=255)
ttCCGTCAACTGTGAGGAAAGTTATGAATACTCGCAGGCAACAGGCCGGGCAAAAGGTAACGCCTGGTTCCAAATTCGCAGGCGACCTgg > 2:397843/1‑90 (MQ=255)
cGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTAc < 2:228795/90‑1 (MQ=255)
ggAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCAc < 2:398242/90‑1 (MQ=255)
aaaGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTg < 1:154873/90‑1 (MQ=255)
cTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTAc < 1:195149/63‑1 (MQ=255)
cTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTAc > 2:195149/1‑63 (MQ=255)
cTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCcgg > 2:178643/1‑90 (MQ=255)
|
TAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGG > NZ_CP009273/1363620‑1363746
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TTACGTAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCC > NZ_CP009273/1363615‑1363743
|
TTACGTAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCT > SRR3722114.188826/1‑100 (MQ=60)
tacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTAC < SRR3722114.398653/50‑1 (MQ=60)
TAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTAC < SRR3722114.95235/100‑1 (MQ=60)
GTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTT < SRR3722114.457908/100‑1 (MQ=60)
atgtgtataagagacagGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGC < SRR3722114.197050/83‑1 (MQ=60)
AAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCC < SRR3722114.156428/100‑1 (MQ=60)
|
TTACGTAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCC > NZ_CP009273/1363615‑1363743
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
