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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
802,549 |
T→G |
T63T (ACA→ACC) |
ybhC ← |
putative acyl‑CoA thioester hydrolase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 802,549 | 0 | T | G | 91.7%
| 31.1
/ ‑3.4
| 12 | T63T (ACA→ACC) | ybhC | putative acyl‑CoA thioester hydrolase |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base G (5/6); total (6/6) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.41e-01 |
TTGAGTGCCCGCCGGGCCGACAACAAAGTCAGGTTGCGCAGGCAGGGTAATCGGGGAAGGATTCCACGCTGCAGCACCTGGTGTCAGGGATGCAAAATAGTGTTGAGCATCGAAATTCTGCGCTTCTTTTGCCGACAGAATCGGGCGAGAAGAGGTACCAGGCGCGGT > NZ_CP009273/802468‑802635
|
ttGAGTGCCCGCCGGGCCGACAACAAAGTCAGGTTGCGCAGGCAGGGTAATCGGGGAAGGATTCCACGCTGCAGCACCTGGGGTCAGGGa > 1:703988/1‑90 (MQ=255)
ttGAGTGCCCGCCGGGCCGACAACAAAGTCAGGTTGCGCAGGCAGGGTAATCGGGGAAGGATTCCACGCTGCAGCACCTGGGGTCAGGGa > 2:370260/1‑90 (MQ=255)
aGTGCCCGCCGGGCCGACAACAAAGTCAGGTTGCGCAGGCAGGGTAATCGGGGAAGGATTCCACGCTGCAGCACCTGGGGTCAGGGATGc < 1:70244/90‑1 (MQ=255)
acgGGCCGACAACAAAGTCAGGTTGCGCAGGCAGGGTAATCGGGGAAGGATTCCACGCTGCAGCACCTGGGGTCAGGGATGCAAAATAgt > 1:354307/2‑90 (MQ=255)
gACAACAAAGTCAGGTTGCGCAGGCAGGGTAATCGGGGAAGGATTCCACGCTGCAGCACCTGGGGTCAGGGATGCAAAATAGTGTTGAGc < 1:534417/90‑1 (MQ=255)
gACAACAAAGTCAGGTTGCGCAGGCAGGGTAATCGGGGAAGGATTCCACGCTGCAGCACCTGGGGTCAGGGATGCAAAATAGTGTTGAGc < 1:569954/90‑1 (MQ=255)
gcgcAGGCAGGGAAATCGGGGAAGGATTCCACGCTGCAGCCCCTGGGGCCAGGGAGGAAAAATGGGGTTGAGCATCGAAATTCTGCGctt > 1:309981/1‑90 (MQ=255)
ggggAAGGATTCCACGCTGCAGCACCTGGGGTCAGGGATGCAAAATAGTGTTGAGCATCGAAATTCTGCGCTTCTTTTGCCGACAGAATc < 1:375276/90‑1 (MQ=255)
ggAAGGATTCCACGCTGCAGCACCTGGGGTCAGGGATGCAAAATAGTGTTGAGCATCGAAATTCTGCGCTTCTTTTGCCGACAGAATCgg > 1:104509/1‑90 (MQ=255)
aTTCCACGCTGCAGCACCTGGGGTCAGGGATGCAAAATAGTGTTGAGCATCGAAATTCTGCGCTTCTTTTGCCGACAGAATCGGGCgaga < 1:370260/90‑1 (MQ=255)
gcaCCTGGGGTCAGGGATGCAAAATAGTGTTGAGCATCGAAATTCTGCGCTTCTTTTGCCGACAGAATCGGGCGAGAAGAGGTACCAGgc < 2:419408/90‑1 (MQ=255)
tGGTGTCAGGGATGCAAAATAGTGTTGAGCATCGAAATTCTGCGCTTCTTTTGCCGACAGAATCGGGCGAGAAGAGGTACCAGGCGCGGt > 2:586137/1‑90 (MQ=255)
|
TTGAGTGCCCGCCGGGCCGACAACAAAGTCAGGTTGCGCAGGCAGGGTAATCGGGGAAGGATTCCACGCTGCAGCACCTGGTGTCAGGGATGCAAAATAGTGTTGAGCATCGAAATTCTGCGCTTCTTTTGCCGACAGAATCGGGCGAGAAGAGGTACCAGGCGCGGT > NZ_CP009273/802468‑802635
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 27 ≤ 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
TGCGTTACACCTTGAGTGCCCGCCGGGCCGACAACAAAGTCAGGTTGCGCAGGCAGGGTAATCGGGGAAGGATTCCACGCTGCAGCACCTGGTGTCAGGGATGCAAAATAGTGTTGAGCATCGAAATTCTGCGCTTCTTTTGCCGACAGAATCGGGCGAGAAGAGGTACCAGGCGCGGTTTGATCAGAAGG > NZ_CP009273/802457‑802647
|
TGCGTTACCCCTTGAGTGCCCGCCGGGCCGACAACAAAGTCAGGTTGCGCAGGCAGGGTAATCGGGGAAGGATTCCACGCTGCAGCACCTGGGGTCAGGG < SRR3722112.403179/100‑1 (MQ=60)
GCGTTACACCTTGAGTGCCCGCCGGGCCGACAACAAAGTCAGGTTGCGCAGGCAGGGTAATCGGGGAAGGATTCCACGCTGCAGCACCTGGGGTCAGGGA > SRR3722112.714982/1‑100 (MQ=60)
TGAGTGCCCGACGGGCCGACAACAAAGTCAGGTTGCGCAGGCAGGGTAATCGGGGAAGGATTCCACGCTGCAGCACCTGGGGTCAGGGATGCAAAATAGT > SRR3722112.358805/1‑100 (MQ=60)
AGTGCCCGCCGGGCCGACAACAAAGTCAGGTTGCGCAGGCAGGGTAATCGGGGAAGGATTCCACGCTGCAGCACCTGGGGTCAGGGATGCAAAATAGTGT < SRR3722112.71097/100‑1 (MQ=60)
GACAACAAAGTCAGGTTGCGCAGGCAGGGTAATCGGGGAAGGATTCCACGCTGCAGCACCTGGGGTCAGGGATGCAAAATAGTGTTGAGCATCGAAATTC < SRR3722112.542361/100‑1 (MQ=60)
GACAACAAAGTCAGGTTGCGCAGGCAGGGTAATCGGGGAAGGATTCCACGCTGCAGCACCTGGGGTCAGGGATGCAAAATAGTGTTGAGCATCGAAATTC < SRR3722112.578637/100‑1 (MQ=60)
AAGTCAGGTTGCGCAGGCAGGGAAATCGGGGAAGGATTCCACGCTGCAGCCCCTGGGGCCAGGGAGGAAAAATGGGGTTGAGCATCGAAATTCTGCGCTT > SRR3722112.313537/1‑100 (MQ=60)
GGGTAATCGGGGAAGGATTCCACGCTGCAGCACCTGGGGTCAGGGATGCAAAATAGTGTTGAGCATCGAAATTCTGCGCTTCTTTTGCCGACAGAATCGG > SRR3722112.105808/1‑100 (MQ=60)
GGGGAAGGATTCCACGCTGCAGCACCTGGGGTCAGGGATGCAAAATAGTGTTGAGCATCGAAATTCTGCGCTTCTTTTGCCGACAGAATCGGGCGAGAAG < SRR3722112.380132/100‑1 (MQ=60)
ATTCCACGCTGCAGCACCTGGGGTCAGGGATGCAAAATAGTGTTGAGCATCGAAATTCTGCGCTTCTTTTGCCGACAGAATCGGGCGAGAAGAGGTACCA < SRR3722112.375045/100‑1 (MQ=60)
TTCCACGCTGCAGCACCTGGGGTCAGGGATGCAAAATAGTGTTGctgtctcttatacacatctgacgctgccgacgaatgtcaatgtgtagatctcggtg > SRR3722112.36764/1‑44 (MQ=60)
CTGCAGCACCTGGGGTCAGGGATGCAAAATAGTGTTGAGCATCGAAATTCTGCGCTTCTTTTGCCGACAGAATCGGGCGAGAAGAGGTACCAGGCGCGGT > SRR3722112.709026/1‑100 (MQ=60)
GGGTCAGGGATGCAAAATAGTGTTGAGCATCGAAATTCTGCGCTTCTTTTGCCGACAGAATCGGGCGAGAAGAGGTACCAGGCGCGGTTTGATCAGAAGG < SRR3722112.82753/100‑1 (MQ=60)
|
TGCGTTACACCTTGAGTGCCCGCCGGGCCGACAACAAAGTCAGGTTGCGCAGGCAGGGTAATCGGGGAAGGATTCCACGCTGCAGCACCTGGTGTCAGGGATGCAAAATAGTGTTGAGCATCGAAATTCTGCGCTTCTTTTGCCGACAGAATCGGGCGAGAAGAGGTACCAGGCGCGGTTTGATCAGAAGG > NZ_CP009273/802457‑802647
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
