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 |
463,972 |
A→G |
D45G (GAC→GGC) |
decR → |
DNA‑binding transcriptional regulator DecR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 463,972 | 0 | A | G | 97.5%
| 122.5
/ ‑4.2
| 40 | D45G (GAC→GGC) | decR | DNA‑binding transcriptional regulator DecR |
| Reads supporting (aligned to +/- strand): ref base A (1/0); new base G (23/16); total (24/16) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.93e-01 |
ATTGCACCCTCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGACGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAACGCAAC > NZ_CP009273/463885‑464058
|
aTTGCACCCTCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAGACGGCTGGAGGacggcg > 1:174431/1‑90 (MQ=255)
ttGCACCCTCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGAcggcgg < 2:1550572/90‑1 (MQ=255)
ttGCACCCTCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGAcggcgg < 1:1516411/90‑1 (MQ=255)
cACCCTCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTAt < 2:746684/90‑1 (MQ=255)
ctctctTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCtt > 2:1157682/1‑90 (MQ=255)
ctctctTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCtt > 2:503902/1‑90 (MQ=255)
tctctTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTa > 2:634938/1‑90 (MQ=255)
ctctTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTAt < 1:132515/90‑1 (MQ=255)
ggCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGG‑AGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTc > 2:677485/1‑90 (MQ=255)
gCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTc > 1:355262/1‑90 (MQ=255)
gCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTc > 2:632057/1‑90 (MQ=255)
gCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTc > 1:271827/1‑90 (MQ=255)
aCTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGc < 2:306551/90‑1 (MQ=255)
tGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGccc > 1:278592/1‑90 (MQ=255)
tGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGccc > 2:1555765/1‑90 (MQ=255)
gAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCctgctg > 1:350296/1‑90 (MQ=255)
gAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCctgctg > 2:1462914/1‑90 (MQ=255)
ccGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATc < 1:516962/90‑1 (MQ=255)
ccGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATc < 2:457936/90‑1 (MQ=255)
gTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGc < 2:1325439/77‑1 (MQ=255)
gTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGc > 1:1325439/1‑77 (MQ=255)
gTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATc > 2:861990/1‑88 (MQ=255)
gTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATc < 1:861990/88‑1 (MQ=255)
aaTCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGaa < 1:546433/90‑1 (MQ=255)
aaTCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGaa < 2:873626/90‑1 (MQ=255)
aTCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGaaa < 1:1572668/90‑1 (MQ=255)
gACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAAt > 2:986219/1‑90 (MQ=255)
gACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAAt > 1:70920/1‑90 (MQ=255)
ccaccCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGACGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGcc > 2:482488/1‑90 (MQ=255)
accCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTc > 2:1295350/1‑90 (MQ=255)
accCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTc > 2:194601/1‑90 (MQ=255)
accCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTc > 2:1420468/1‑90 (MQ=255)
cTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGcc < 1:1025701/90‑1 (MQ=255)
cTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGcc < 1:302242/90‑1 (MQ=255)
tGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGAcc < 1:503902/90‑1 (MQ=255)
gAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCg > 1:63535/1‑50 (MQ=255)
gAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCg < 2:63535/50‑1 (MQ=255)
gcCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTtg > 2:753958/1‑90 (MQ=255)
gcCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTtg > 1:645482/1‑90 (MQ=255)
gAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCt > 2:824896/1‑90 (MQ=255)
cGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATa > 2:490986/1‑90 (MQ=255)
ggaggaCGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAAc < 1:1451406/90‑1 (MQ=255)
ggaCGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAACGCa < 1:634938/90‑1 (MQ=255)
acggcgGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAACGCAAc < 2:645482/90‑1 (MQ=255)
acggcgGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAACGCAAc < 1:227190/90‑1 (MQ=255)
acggcgGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAACGCAAc < 1:1462914/90‑1 (MQ=255)
|
ATTGCACCCTCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGACGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAACGCAAC > NZ_CP009273/463885‑464058
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ 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
CTGCAGCAGGATTGCACCCTCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGACGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAACGCAACATCACAGCAGCGA > NZ_CP009273/463875‑464071
|
CTGCAGCAGGATTGCACCCTCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAGACGGCTGGAGGACGGCG > SRR3722078.176476/1‑100 (MQ=60)
CAGGATTGCACCCTCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCC < SRR3722078.1039437/100‑1 (MQ=60)
CAGGATTGCACCCTCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCC < SRR3722078.753899/100‑1 (MQ=60)
CAGGATTGCACCCTCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCC < SRR3722078.639590/100‑1 (MQ=60)
GATTGCACCCTCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCctg > SRR3722078.524718/1‑97 (MQ=60)
TTGCACCCTCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATC < SRR3722078.1541147/100‑1 (MQ=60)
CTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTC < SRR3722078.134046/100‑1 (MQ=60)
CTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTC > SRR3722078.359591/1‑100 (MQ=60)
CTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTC > SRR3722078.275144/1‑100 (MQ=60)
TTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCC > SRR3722078.281995/1‑100 (MQ=60)
aaatctacacgaccgccatcgtcggcagcgtcagatgtgtataagagacagGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTG < SRR3722078.1052409/49‑1 (MQ=60)
GGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTG > SRR3722078.354590/1‑100 (MQ=60)
GGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCCGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCTG > SRR3722078.1346629/1‑100 (MQ=60)
CCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAAT < SRR3722078.873524/100‑1 (MQ=60)
CCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAAT > SRR3722078.71750/1‑100 (MQ=60)
CCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAAT < SRR3722078.523078/100‑1 (MQ=60)
AATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCC < SRR3722078.552881/100‑1 (MQ=60)
ATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCT < SRR3722078.1598266/100‑1 (MQ=60)
CCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGActgtctcttatacacatctgacgctgccga > SRR3722078.64281/1‑70 (MQ=60)
CTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTT < SRR3722078.305933/100‑1 (MQ=60)
CTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTT < SRR3722078.1040912/100‑1 (MQ=60)
TGCTGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTG > SRR3722078.652902/1‑100 (MQ=60)
TGGAAGCGCCTGAAACGGCTGGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGC < SRR3722078.509857/100‑1 (MQ=60)
GGAGGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAACGCAACATCAC < SRR3722078.1475076/100‑1 (MQ=60)
GGACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAACGCAACATCACAGC < SRR3722078.642234/100‑1 (MQ=60)
ACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAACGCAACATCACAGCAG < SRR3722078.229947/100‑1 (MQ=60)
ACGGCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAACGCAACATCACAGCAG < SRR3722078.1486784/100‑1 (MQ=60)
GCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAACGCAACATCACAGCAGCGA > SRR3722078.1413636/1‑100 (MQ=60)
GCGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAACGCAACATCACAGCAGCGA > SRR3722078.1211971/1‑100 (MQ=60)
|
CTGCAGCAGGATTGCACCCTCTCTTTGCAGGCACTGGCTGAAGCCGTTAATCTGACAACCACCCCTTGCTGGAAGCGCCTGAAACGGCTGGAGGACGACGGTATCCTTATCGGCAAAGTCGCCCTGCTGGATCCGGAAAAAATAGGCCTCGGCCTGACCGCTTTTGTGCTGATAAAAACGCAACATCACAGCAGCGA > NZ_CP009273/463875‑464071
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
