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 |
1,900,885 |
A→G |
S145P (TCC→CCC) |
rlmA ← |
23S rRNA (guanine(745)‑N(1))‑methyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,900,885 | 0 | A | G | 97.9%
| 151.3
/ ‑3.9
| 48 | S145P (TCC→CCC) | rlmA | 23S rRNA (guanine(745)‑N(1))‑methyltransferase |
| Reads supporting (aligned to +/- strand): ref base A (1/0); new base G (30/17); total (31/17) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.51e-01 |
CCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGAAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAACA > NZ_CP009273/1900799‑1900970
|
ccAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGgaaa < 1:140027/90‑1 (MQ=255)
ccAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGgaaa > 1:195884/1‑90 (MQ=255)
aGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACg > 2:1260546/1‑90 (MQ=255)
aGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACg > 1:78521/1‑90 (MQ=255)
aGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACg > 1:1280277/1‑90 (MQ=255)
aGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACg > 1:1323048/1‑90 (MQ=255)
aGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACg > 1:1562956/1‑90 (MQ=255)
aGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACCGGTATCGGGAAACg > 1:573838/1‑90 (MQ=255)
ggCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACgg < 2:19858/90‑1 (MQ=255)
tctGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCg > 1:535047/1‑78 (MQ=255)
tctGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCg < 2:535047/78‑1 (MQ=255)
tctGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGAcaca < 2:693085/83‑1 (MQ=255)
tctGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGAcaca > 1:693085/1‑83 (MQ=255)
tctGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTg > 2:317076/1‑90 (MQ=255)
tctGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTg < 2:641237/90‑1 (MQ=255)
tGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGAc < 1:828021/90‑1 (MQ=255)
gCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGAcc < 1:914357/90‑1 (MQ=255)
cTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCt < 2:1112204/90‑1 (MQ=255)
cTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCt < 2:1073184/90‑1 (MQ=255)
cTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGCGGCTGGAAGCGACACAAAAAGTGACCt < 2:1323048/90‑1 (MQ=255)
ttACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGc > 1:1500716/1‑90 (MQ=255)
ttACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGc > 1:1480821/1‑90 (MQ=255)
ttACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGc > 1:1158358/1‑90 (MQ=255)
ttACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGc < 2:1480821/90‑1 (MQ=255)
acGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGAt < 1:123450/90‑1 (MQ=255)
cGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATa < 2:1007492/90‑1 (MQ=255)
gcgcGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGc > 1:770362/1‑90 (MQ=255)
gcgcGTAAATACGTATTATGGCGTCCATACTGGTATCGGAAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGc > 1:353422/1‑90 (MQ=255)
gcgcGTAAATACGTATTATGGCGTCCATACTGGGATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGc > 1:218727/1‑90 (MQ=255)
aCGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTcgccgc > 1:598644/1‑90 (MQ=255)
ttatGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCtt > 1:35025/1‑90 (MQ=255)
tatGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCttt > 1:1215747/1‑90 (MQ=255)
gTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTcgccgcc < 2:976437/79‑1 (MQ=255)
gTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTcgccgcc > 1:976437/1‑79 (MQ=255)
gTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTc < 1:665785/73‑1 (MQ=255)
gTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTc > 2:665785/1‑73 (MQ=255)
gTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGc > 2:701596/1‑90 (MQ=255)
gTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGc > 2:1375186/1‑90 (MQ=255)
gTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGc > 1:422987/1‑90 (MQ=255)
gTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGc > 2:37629/1‑90 (MQ=255)
gTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGc > 2:409690/1‑90 (MQ=255)
gTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGc > 2:515267/1‑90 (MQ=255)
gTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGc > 1:1312882/1‑90 (MQ=255)
aCTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCtt < 1:193096/90‑1 (MQ=255)
ggTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCt < 2:1141397/86‑1 (MQ=255)
ggTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCt > 1:1141397/1‑86 (MQ=255)
gTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGaa > 1:967995/1‑90 (MQ=255)
gTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGaa < 2:1158358/90‑1 (MQ=255)
aTCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAAc > 1:1133432/1‑90 (MQ=255)
tCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAACa > 2:650691/1‑90 (MQ=255)
|
CCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGAAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAACA > NZ_CP009273/1900799‑1900970
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ 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
GGCAGTAATGACCCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGAAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAACATCCAGACC > NZ_CP009273/1900787‑1900978
|
cgaccgccatcgtcggcagcgtcagatgtgtataagagacagTTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGA < SRR3722078.360699/58‑1 (MQ=60)
GGCAGTAATGACCCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGA < SRR3722078.501826/100‑1 (MQ=60)
CAGTAATGACCCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAA > SRR3722078.198219/1‑100 (MQ=60)
GTAATGACCCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACG > SRR3722078.1300640/1‑100 (MQ=60)
GTAATGACCCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACG > SRR3722078.79447/1‑100 (MQ=60)
GTAATGACCCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACG > SRR3722078.1344198/1‑100 (MQ=60)
GTAATGACCCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACG > SRR3722078.1588400/1‑100 (MQ=60)
GTAATGACCCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACCGGTATCGGGAAACG > SRR3722078.580542/1‑100 (MQ=60)
CCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGG < SRR3722078.141659/100‑1 (MQ=60)
TGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGct > SRR3722078.541369/1‑98 (MQ=60)
TGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTG > SRR3722078.701322/1‑100 (MQ=60)
TTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGC > SRR3722078.1504971/1‑100 (MQ=60)
TTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGC > SRR3722078.1525189/1‑100 (MQ=60)
TTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGC > SRR3722078.1176286/1‑100 (MQ=60)
TGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAG < SRR3722078.839003/100‑1 (MQ=60)
GCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGC < SRR3722078.926763/100‑1 (MQ=60)
GCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGC > SRR3722078.780297/1‑100 (MQ=60)
GCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGAAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGC > SRR3722078.357733/1‑100 (MQ=60)
GCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGGATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGC > SRR3722078.221370/1‑100 (MQ=60)
ACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGC < SRR3722078.124887/100‑1 (MQ=60)
GCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGC > SRR3722078.605574/1‑100 (MQ=60)
gagacagGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTT < SRR3722078.673408/93‑1 (MQ=60)
TAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTT > SRR3722078.35454/1‑100 (MQ=60)
AAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTT > SRR3722078.1234857/1‑100 (MQ=60)
GTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGC > SRR3722078.990471/1‑100 (MQ=60)
GTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGC > SRR3722078.428087/1‑100 (MQ=60)
GTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGC > SRR3722078.1333854/1‑100 (MQ=60)
CGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGA > SRR3722078.1158952/1‑100 (MQ=60)
GTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAA > SRR3722078.981816/1‑100 (MQ=60)
CCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAAC > SRR3722078.1150793/1‑100 (MQ=60)
ACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAACATCC < SRR3722078.195396/100‑1 (MQ=60)
GGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAACATCCAGA > SRR3722078.632879/1‑100 (MQ=60)
TATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAACATCCAGACC < SRR3722078.757826/100‑1 (MQ=60)
|
GGCAGTAATGACCCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGAAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAACATCCAGACC > NZ_CP009273/1900787‑1900978
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
