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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,259,173 |
A→G |
T2A (ACC→GCC) |
hemA → |
glutamyl‑tRNA reductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,259,173 | 0 | A | G | 94.7%
| 111.1
/ ‑2.1
| 38 | T2A (ACC→GCC) | hemA | glutamyl‑tRNA reductase |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base G (26/10); total (27/11) |
| Fisher's exact test for biased strand distribution p-value = 5.01e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GGGCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGGCG > NZ_CP009273/1259086‑1259262
|
gggCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGcc > 1:1140746/1‑90 (MQ=255)
ttATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCATTTTAGCACTc < 2:877433/90‑1 (MQ=255)
gATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTAt > 1:410428/1‑90 (MQ=255)
aTCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATc < 2:179975/90‑1 (MQ=255)
tCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCa < 1:791571/90‑1 (MQ=255)
tCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCa < 1:553898/90‑1 (MQ=255)
tCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCa < 1:1212881/90‑1 (MQ=255)
ttACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGGCATGGCCCTTTTAGCACTCGGTATCAAc > 2:213681/1‑90 (MQ=255)
tCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATaaaa > 2:104560/1‑90 (MQ=255)
gTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGc > 1:1189631/1‑90 (MQ=255)
atgCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTc > 1:504885/1‑65 (MQ=255)
atgCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTc < 2:504885/65‑1 (MQ=255)
cAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTAt > 1:943980/1‑90 (MQ=255)
aaGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATc < 2:691710/90‑1 (MQ=255)
aGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTc > 1:515822/1‑60 (MQ=255)
aGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTc < 2:515822/60‑1 (MQ=255)
aGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCg > 2:153073/1‑90 (MQ=255)
aGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCg > 2:1284713/1‑90 (MQ=255)
aGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCg > 2:622827/1‑90 (MQ=255)
aGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCg > 1:261648/1‑90 (MQ=255)
gACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACt > 2:263601/1‑55 (MQ=255)
gACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACt < 1:263601/55‑1 (MQ=255)
aCTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCg > 1:1488689/1‑90 (MQ=255)
cTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTc > 1:849713/1‑54 (MQ=255)
cTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTc < 2:849713/54‑1 (MQ=255)
cTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCga > 1:520849/1‑90 (MQ=255)
tATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACgtg > 1:1090141/1‑90 (MQ=255)
aTCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACgtgt > 2:191511/1‑90 (MQ=255)
aTCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACgtgt > 1:271591/1‑90 (MQ=255)
aTCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACgtgt > 2:1477784/1‑90 (MQ=255)
aCGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCg > 2:171556/1‑90 (MQ=255)
aCGTTGGGATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCg > 2:760386/1‑90 (MQ=255)
gTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGtt > 1:1485328/1‑90 (MQ=255)
tGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGtttt > 2:1063938/1‑90 (MQ=255)
cccGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAg < 1:565858/90‑1 (MQ=255)
ccGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGc > 1:912548/1‑90 (MQ=255)
ccGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGc > 1:359725/1‑90 (MQ=255)
ccGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGc > 1:1373205/1‑90 (MQ=255)
aCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGgcg < 1:646016/90‑1 (MQ=255)
|
GGGCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGGCG > NZ_CP009273/1259086‑1259262
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ 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
CTCCAAAAGGGGGCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGGCGCTTGACAGCC > NZ_CP009273/1259076‑1259272
|
CTCCAAAAGGGGGCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCC > SRR3722078.1158279/1‑100 (MQ=60)
CTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTAT > SRR3722078.415387/1‑100 (MQ=60)
agcgtcagatgtgtataagagacagGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAAC < SRR3722078.266819/75‑1 (MQ=60)
TCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAAC < SRR3722078.801936/100‑1 (MQ=60)
TCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAAC < SRR3722078.560431/100‑1 (MQ=60)
TCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCAACCATAAAAC < SRR3722078.1231950/100‑1 (MQ=60)
TACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGC > SRR3722078.1208228/1‑100 (MQ=60)
ATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCctgtctcttatacac > SRR3722078.510857/1‑85 (MQ=60)
CTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTAT > SRR3722078.957153/1‑100 (MQ=60)
GTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCctgtctcttatacacatctg > SRR3722078.521927/1‑80 (MQ=60)
GTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCG > SRR3722078.264842/1‑100 (MQ=60)
ATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCG > SRR3722078.1512950/1‑100 (MQ=60)
TGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCctgtctcttatacacatctgacgctg > SRR3722078.861053/1‑74 (MQ=60)
TGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGA > SRR3722078.527009/1‑100 (MQ=60)
AGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTG > SRR3722078.1106680/1‑100 (MQ=60)
GACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGT > SRR3722078.274903/1‑100 (MQ=60)
CCCTATCAACGTTGGTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTT > SRR3722078.1509544/1‑100 (MQ=60)
GTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGC > SRR3722078.364106/1‑100 (MQ=60)
GTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGC > SRR3722078.1395337/1‑100 (MQ=60)
GTATTATTTCCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGC > SRR3722078.924899/1‑100 (MQ=60)
CCCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGG < SRR3722078.572489/100‑1 (MQ=60)
CCGCAGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGGC > SRR3722078.1569520/1‑100 (MQ=60)
cagGACATGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGGCGC < SRR3722078.1095456/97‑1 (MQ=60)
TGGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGGCGCTTGACAG > SRR3722078.1478647/1‑100 (MQ=60)
GGCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGGCGCTTGACAGC < SRR3722078.1451991/100‑1 (MQ=60)
GCCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGGCGCTTGACAGCC < SRR3722078.1343918/100‑1 (MQ=60)
ACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGGCGCTTGACAGCC < SRR3722078.653444/100‑1 (MQ=60)
|
CTCCAAAAGGGGGCGCTCTCTTTTATTGATCTTACGCATCCTGTATGATGCAAGCAGACTAACCCTATCAACGTTGGTATTATTTCCCGCAGACATGACCCTTTTAGCACTCGGTATCAACCATAAAACGGCACCTGTATCGCTGCGAGAACGTGTATCGTTTTCGCCGGATAAGCTCGATCAGGCGCTTGACAGCC > NZ_CP009273/1259076‑1259272
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
