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 |
2,849,315 |
A→C |
Y540S (TAC→TCC) |
flhA → |
formate hydrogenlyase transcriptional activator FlhA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,849,315 | 0 | A | C | 96.4%
| 85.2
/ ‑3.6
| 28 | Y540S (TAC→TCC) | flhA | formate hydrogenlyase transcriptional activator FlhA |
| Reads supporting (aligned to +/- strand): ref base A (1/0); new base C (14/13); total (15/13) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01 |
TTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACC > NZ_CP009273/2849228‑2849397
|
ttCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTccc < 2:1516179/90‑1 (MQ=255)
ttCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTccc < 1:1504461/90‑1 (MQ=255)
gacgTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAAc > 2:845295/1‑90 (MQ=255)
acgTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACg < 2:1580210/90‑1 (MQ=255)
acgTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACg > 2:1181634/1‑90 (MQ=255)
gCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTAtt > 2:46293/1‑90 (MQ=255)
gCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTAtc > 1:1442250/1‑89 (MQ=255)
cGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTc < 2:1386582/90‑1 (MQ=255)
ccgcGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCAcc > 1:1500879/1‑90 (MQ=255)
ccgcGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCAcc > 1:883095/1‑90 (MQ=255)
gcgACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTg > 2:398193/1‑90 (MQ=255)
cgACCACCCGCGTTCTGAAAAAAAGGGCCGCCGCCCGTGAGTTCCGTAGCGTTCTTTATTCCCGCCTGAACGTATTCCCGATTCACCTgc < 1:1323218/90‑1 (MQ=255)
gACTACCCGCGATCTAAAAAAAATGGTCCCCGCCCGTGAGTTCCGTAGCGATCTCTTTTCCCGCCTGAACGTATTCCCGATTCCCCTgcc < 1:845295/90‑1 (MQ=255)
ccTACCCGCGATCTGAAAAAAATGGTCGCCGCCCGTGAGTTCCGTAGCGATCTCTTTTCCCGCCTGAACGTATTCCCGATTCACCTgccg < 1:21155/89‑1 (MQ=255)
gATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTAcgc > 2:1521642/1‑90 (MQ=255)
gATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTAcgc > 1:424003/1‑90 (MQ=255)
aTCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTccc > 2:895734/1‑51 (MQ=255)
aTCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTccc < 1:895734/51‑1 (MQ=255)
tGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGc < 1:398193/90‑1 (MQ=255)
aaaaaaaaTGGTCCCCGCCCGTGATTCCCGTAGCGATCTCTTTCCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCg < 1:1022746/89‑1 (MQ=255)
aaaaTGGTCGCCGCCCGTGATTCCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCg < 1:27492/90‑1 (MQ=255)
aTGGTCGCCGCCCGTGATTCCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGaa < 1:292037/90‑1 (MQ=255)
gTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGat > 2:916034/1‑90 (MQ=255)
gTCGCCGACCGTGAGTCCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGat < 2:349542/90‑1 (MQ=255)
gAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGctgctg > 1:1054185/1‑90 (MQ=255)
ccGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCCCCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGaa < 2:1374572/90‑1 (MQ=255)
ccGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGaa < 1:1521642/90‑1 (MQ=255)
gTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAg > 1:617965/1‑90 (MQ=255)
gATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCttt > 1:711900/1‑90 (MQ=255)
aTCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTa > 1:165879/1‑90 (MQ=255)
ctctATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTAcc > 2:1095832/1‑90 (MQ=255)
aTTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAg < 2:620212/47‑1 (MQ=255)
|
TTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACC > NZ_CP009273/2849228‑2849397
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GCAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTGCCCG > NZ_CP009273/2849216‑2849411
|
GCAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTC < SRR3722078.1158886/100‑1 (MQ=60)
agcgtcagatgtgtataagagacaGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCC < SRR3722078.1026175/76‑1 (MQ=60)
CATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAAC < SRR3722078.1404279/100‑1 (MQ=60)
cggcagcgtcagatgtgtataagagacaGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGT < SRR3722078.907767/72‑1 (MQ=60)
TTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGT < SRR3722078.1529005/100‑1 (MQ=60)
AGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATC > SRR3722078.1465733/1‑100 (MQ=60)
CGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACC > SRR3722078.894962/1‑100 (MQ=60)
CGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACC > SRR3722078.1525355/1‑100 (MQ=60)
CGACCACCCGCGTTCTGAAAAAAAGGGCCGCCGCCCGTGAGTTCCGTAGCGTTCTTTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACG < SRR3722078.1344371/100‑1 (MQ=60)
GACTACCCGCGATCTAAAAAAAATGGTCCCCGCCCGTGAGTTCCGTAGCGATCTCTTTTCCCGCCTGAACGTATTCCCGATTCCCCTGCCGCCACTACGC < SRR3722078.856577/100‑1 (MQ=60)
GACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGC > SRR3722078.429111/1‑100 (MQ=60)
cctacCCGCGATCTGAAAAAAATGGTCGCCGCCCGTGAGTTCCGTAGCGATCTCTTTTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCG < SRR3722078.21423/95‑1 (MQ=60)
TAAAAAAAATGGTCGCCGCCCGTGAGTCCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGA < SRR3722078.403025/100‑1 (MQ=60)
AAAAAAAATGGTCCCCGCCCGTGATTCCCGTAGCGATCTCTTTCCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGAT < SRR3722078.1037895/100‑1 (MQ=60)
AAAATGGTCGCCGCCCGTGATTCCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTC < SRR3722078.27835/100‑1 (MQ=60)
ATGGTCGCCGCCCGTGATTCCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGC < SRR3722078.295602/100‑1 (MQ=60)
CGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTG > SRR3722078.1070015/1‑100 (MQ=60)
CGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAG > SRR3722078.625089/1‑100 (MQ=60)
GTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTT > SRR3722078.720613/1‑100 (MQ=60)
TTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTA > SRR3722078.167810/1‑100 (MQ=60)
CCGTAGCGATCTCTATCCCCGCCTGAACGTATTCCCGATTCCCCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACC < SRR3722078.1546453/100‑1 (MQ=60)
AGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGctgtctcttatacacatctgacgctgccgacga > SRR3722078.627355/1‑67 (MQ=60)
AGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCA > SRR3722078.78345/1‑100 (MQ=60)
GATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAA > SRR3722078.111725/1‑100 (MQ=60)
CTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTG > SRR3722078.1208425/1‑100 (MQ=60)
CTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTG > SRR3722078.908269/1‑100 (MQ=60)
ATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATctgtct > SRR3722078.1334988/1‑94 (MQ=60)
|
GCAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTGCCCG > NZ_CP009273/2849216‑2849411
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
