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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
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%
| 34.7
/ NA
| 11 | F16S (TTC→TCC) | pspD | phage shock protein PspD |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (3/8); total (3/8) |
TAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAGTT > NZ_CP009273/1363620‑1363778
|
tAGCCGTTTCCGTCAACTGTGAGGAAAGTTTTGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCGAAATTCGCAGGc < 1:528935/90‑1 (MQ=255)
tAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGTCTGGTTCCAAATTAGCAGGc < 2:223899/90‑1 (MQ=255)
ttCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTgg > 1:116369/1‑90 (MQ=255)
tCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGt < 1:249653/90‑1 (MQ=255)
tCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTActt < 2:710401/90‑1 (MQ=255)
tgtgAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTAc < 2:755261/90‑1 (MQ=255)
gtgAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTAcc > 2:172623/1‑90 (MQ=255)
gAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACt < 1:356084/90‑1 (MQ=255)
ggCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGc > 1:655400/1‑35 (MQ=255)
ggCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGc < 2:655400/35‑1 (MQ=255)
ccTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAGtt < 1:354237/90‑1 (MQ=255)
|
TAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAGTT > NZ_CP009273/1363620‑1363778
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 31 ≤ 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
CGATACTTTCACGTTACGTAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAGTTGCTCGCCGAC > NZ_CP009273/1363602‑1363788
|
CGATTCTTTCACGTTACGTAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTCCCAAAT < SRR3722073.179197/100‑1 (MQ=60)
ACGTAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGG > SRR3722073.118857/1‑100 (MQ=60)
TAGCCGTTTCCGTCAACTGTGAGGAAAGTTTTGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCGAAATTCGCAGGCAAGCTGGTAC < SRR3722073.540006/100‑1 (MQ=60)
TCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACC < SRR3722073.254899/100‑1 (MQ=60)
GAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGC < SRR3722073.363620/100‑1 (MQ=60)
CAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACctgtctcttatacacatctgacgctgccgacgatatgcagtgtgt > SRR3722073.668846/1‑55 (MQ=60)
AAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGGGTGGCGGGgggggggggaaaaataagtt > SRR3722073.756610/1‑80 (MQ=60)
GGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGgggggcggggggggggggaaaaaaaaattgt > SRR3722073.706657/1‑69 (MQ=60)
AGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGCGTGGCGGGgcggggggtgaaaacctgtctttttta > SRR3722073.429520/1‑73 (MQ=60)
CCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAGTTGCTCGCCGAC < SRR3722073.361736/100‑1 (MQ=60)
|
CGATACTTTCACGTTACGTAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAGTTGCTCGCCGAC > NZ_CP009273/1363602‑1363788
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
