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 I211 R1
|
223 |
18.0 |
1007644 |
96.3% |
970361 |
85.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,673,542 |
A→G |
K287E (AAG→GAG) |
ydgH → |
DUF1471 family protein YdgH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,673,542 | 0 | A | G | 93.8%
| 42.3
/ NA
| 16 | K287E (AAG→GAG) | ydgH | DUF1471 family protein YdgH |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (4/11); total (4/12) |
| 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 |
ATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCG > NZ_CP009273/1673458‑1673611
|
atgGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGaaa < 1:74284/90‑1 (MQ=255)
cGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTa > 1:164116/1‑90 (MQ=255)
cGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTa < 2:103222/90‑1 (MQ=255)
cGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTa < 2:55838/90‑1 (MQ=255)
gTTCGACAGCATCAAATTCTCTGGCAACTCCGGCAACATGACCGAAGTCTCCTATCAGGTTGCTAAACGTGCCGCGGAGAAAGGTGCTaa < 1:312073/90‑1 (MQ=255)
gTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTaa < 1:207296/90‑1 (MQ=255)
gTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTaa < 1:220869/90‑1 (MQ=255)
ttCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAg < 1:230495/90‑1 (MQ=255)
aCAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTAtt < 2:164116/90‑1 (MQ=255)
ctGGCAACTACGGCAACATGACCGAAGTCTCCTGTCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGcc > 1:493503/1‑90 (MQ=255)
ctGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCt > 1:197195/1‑68 (MQ=255)
ctGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCt < 2:197195/68‑1 (MQ=255)
aaCATGCCCGAAGTCTCCAATCAGGTTGCAAAACGTGCCGCGGAAAAAGGTGCAAATTATTCCCACATCCCCCGCCAGTGGCAGGAACGt < 1:56226/90‑1 (MQ=255)
aaCATGCCAGAAGCCTCCTACAAGGTGGCAAACGGTGGCGGGAAGAAAGGTACTAATTATTCCCACACCCCCCGCCAGTGGCAGGAACGt < 1:445309/90‑1 (MQ=255)
tATCGGGTTGCGAACCGTGCCGGGGAGAAAGGTGCTAAGTTTTACCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTc < 2:118417/90‑1 (MQ=255)
aGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAgcg > 2:190732/1‑90 (MQ=255)
|
ATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCG > NZ_CP009273/1673458‑1673611
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 17 ≤ 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
ATGATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACC > NZ_CP009273/1673455‑1673599
|
ATGATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTA > SRR3722094.166409/1‑100 (MQ=60)
ATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGT < SRR3722094.75344/100‑1 (MQ=60)
GTTCGACAGCATCAAATTCTCTGGCAACTCCGGCAACATGACCGAAGTCTCCTATCAGGTTGCTAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCAC < SRR3722094.316974/100‑1 (MQ=60)
GTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCAC < SRR3722094.210097/100‑1 (MQ=60)
GTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCAC < SRR3722094.223836/100‑1 (MQ=60)
TTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACA < SRR3722094.233680/100‑1 (MQ=60)
ATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTGTCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCC > SRR3722094.502202/1‑100 (MQ=60)
ATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCctgtctcttata > SRR3722094.199890/1‑88 (MQ=60)
aacatgccagaagcctcctacaaggtggcaaacggtggcggGAAGAAAGGTACTAATTATTCCCACACCCCCCGCCAGTGGCAGGAACGTGGTAATAACC < SRR3722094.453142/59‑1 (MQ=34)
AACATGCCCGAAGTCTCCAATCAGGTTGCAAAACGTGCCGCGGAAAAAGGTGCAAATTATTCCCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACC < SRR3722094.57004/100‑1 (MQ=60)
|
ATGATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACC > NZ_CP009273/1673455‑1673599
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
