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 F4 I88 R1
|
217 |
30.5 |
1742422 |
95.9% |
1670982 |
87.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
455,525 |
C→T |
H394H (CAC→CAT) |
lon → |
endopeptidase La |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 455,525 | 0 | C | T | 95.0%
| 62.6
/ ‑3.5
| 20 | H394H (CAC→CAT) | lon | endopeptidase La |
| Reads supporting (aligned to +/- strand): ref base C (1/0); new base T (12/7); total (13/7) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.19e-01 |
GTCAGTCCATTGCCAAAGCCACCGGGCGTAAATATGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCACCGCCGTACTTACATCGGTTCTATGCCGGGTAAACTGATCCAGAAAATGGCGAAAGTGGGCGTGAAAAACCCGC > NZ_CP009273/455440‑455598
|
gTCAGTCCATTGCCAAAGCCACCGGGCGTAAATATGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCAtcgccg < 1:401405/91‑1 (MQ=255)
tCCATTGCCAAAGCCACCGGGCGTAAATATGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACtt < 1:309253/91‑1 (MQ=255)
tCCATTGCCAAAGCCACCGGGCGTAAATATGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACtt < 2:266260/91‑1 (MQ=255)
tgacAAAGCCGCAGGGCATAAAGATGTCCGTATGGCGCTGGGCGGCCTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACTTACATc < 2:312739/88‑1 (MQ=255)
tGCCAAAGCCACCGGGCGTAAATATGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACTTACATc < 1:670495/91‑1 (MQ=255)
tGCCAAAGCCACCGGGCGTAAATATGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACTTACATc < 2:360426/91‑1 (MQ=255)
aaaGCCACCGGGCGTAAATATGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACTTACATCGGtt > 2:694043/1‑91 (MQ=255)
aaaGCCACCGGGCGTAAATATGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACTTACATCGGtt > 2:420112/1‑91 (MQ=255)
aCCGGGCGTAAATATGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACTTACATCGGTTCTATGc > 2:531632/1‑91 (MQ=255)
ccGGGCGTAAATATGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACTTACATCGGTTCTATGcc > 2:68998/1‑91 (MQ=255)
cGGGCGTAAATATGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACTTACATCGGTTCTATGCCg < 1:653515/91‑1 (MQ=255)
gTAAATATGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACTTACATCGGTTCTATGCCGGGTaa > 2:14525/1‑91 (MQ=255)
tGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACTTACATCGGTTCTATGCCGGGTAAACTGATc > 1:448420/1‑91 (MQ=255)
tGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACTTACATCGGTTCTATGCCGGGTAAACTGATc > 2:576339/1‑91 (MQ=255)
tGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCACCGCCGTACTTACATCGGTTCTATGCCGGGTAAACTGATc > 2:335808/1‑91 (MQ=255)
gTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACTTACATCGGTTCTATGCCGGGTAAACTGATcc > 2:367076/1‑91 (MQ=255)
gTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACTTACATCGGTTCTATGCCGGGTAAACTGATCCAGaa > 2:255334/1‑91 (MQ=255)
ggCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACTTACATCGGTTCTATGCCGGGTAAACTGATCCAGAAAATg > 1:174982/1‑91 (MQ=255)
gcgcTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACTTACATCGGTTCTATGCCGGGTAAACTGATCCAGAAAATgg > 1:480843/1‑91 (MQ=255)
tGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACTTACATCGGTTCTATGCCGGGTAAACTGATCCAGAAAATGGCGaa > 2:769330/1‑91 (MQ=255)
gCGGAAATCCGTGGTCATCGCCGTACTTACATCGGTTCTATGCCGGGTAAACTGATCCAGAAAATGGCGAAAGTGGGCGTGAAAAACCCGc < 1:423319/91‑1 (MQ=255)
|
GTCAGTCCATTGCCAAAGCCACCGGGCGTAAATATGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCACCGCCGTACTTACATCGGTTCTATGCCGGGTAAACTGATCCAGAAAATGGCGAAAGTGGGCGTGAAAAACCCGC > NZ_CP009273/455440‑455598
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ 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
GTCAGTCCATTGCCAAAGCCACCGGGCGTAAATATGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCACCGCCGTACTTACATCGGTTCTATGCCGGGTAAACTGATCCAGAAAATGGCGAAAGTGGGCGTGAAAAACCCGCTGTTCCTGCT > NZ_CP009273/455440‑455608
|
GTCAGTCCATTGCCAAAGCCACCGGGCGTAAATATGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACTTACATC < SRR3722118.409831/101‑1 (MQ=60)
TCCATTGCCAAAGCCACCGGGCGTAAATATGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACTTACATCGGTTC < SRR3722118.315606/101‑1 (MQ=60)
TGCCAAAGCCACCGGGCGTAAATATGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACTTACATCGGTTCTATGC < SRR3722118.685027/101‑1 (MQ=60)
CGGGCGTAAATATGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACTTACATCGGTTCTATGCCGGGTAAACTGA < SRR3722118.667636/101‑1 (MQ=60)
GGCGTAAATATGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACTTACATCGGTTCTATGCCGGGTAAACTGATC > SRR3722118.457886/1‑101 (MQ=60)
ATGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACTTACATCGGTTCTATGCCGGGTAAACTGATCCAGAAAATG > SRR3722118.178410/1‑101 (MQ=60)
TGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCATCGCCGTACTTACATCGGTTCTATGCCGGGTAAACTGATCCAGAAAATGG > SRR3722118.491024/1‑101 (MQ=60)
GCGGAAATCCGTGGTCATCGCCGTACTTACATCGGTTCTATGCCGGGTAAACTGATCCAGAAAATGGCGAAAGTGGGCGTGAAAAACCCGCTGTTCCTGCT < SRR3722118.432268/101‑1 (MQ=60)
|
GTCAGTCCATTGCCAAAGCCACCGGGCGTAAATATGTCCGTATGGCGCTGGGCGGCGTGCGTGATGAAGCGGAAATCCGTGGTCACCGCCGTACTTACATCGGTTCTATGCCGGGTAAACTGATCCAGAAAATGGCGAAAGTGGGCGTGAAAAACCCGCTGTTCCTGCT > NZ_CP009273/455440‑455608
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
