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 I231 R1	218	12.8	703680	97.2%	683976	86.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,102,646	T→C	G140G (GGA→GGG)	wzx ←	O16 family O‑antigen flippase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,102,646	0	T	C	100.0%	33.6 / NA	11	G140G (GGA→GGG)	wzx	O16 family O‑antigen flippase
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (6/5); total (6/5)

TTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTTCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTATATTC  >  NZ_CP009273/2102561‑2102732

ttGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCt                                                                                    >  1:241999/1‑90 (MQ=255)

   tgtTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGaa                                                                                 <  2:323082/90‑1 (MQ=255)

                                 taGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGAt                                                                       >  1:85845/1‑70 (MQ=255)

                                 taGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGAt                                                                       <  2:85845/70‑1 (MQ=255)

                                 taGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGa                                                   >  2:60221/1‑90 (MQ=255)

                                                      tactTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGAcc                              <  2:291353/90‑1 (MQ=255)

                                                       actTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCa                             >  1:73693/1‑90 (MQ=255)

                                                            aaGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATaa                        >  2:65578/1‑90 (MQ=255)

                                                                 aGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACaa                                    <  1:348443/73‑1 (MQ=255)

                                                                 aGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACaa                                    >  2:348443/1‑73 (MQ=255)

                                                                        tcatttTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCt            <  1:51866/90‑1 (MQ=255)

                                                                                  tttccCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTATATTc  <  2:73693/90‑1 (MQ=255)

TTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTTCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTATATTC  >  NZ_CP009273/2102561‑2102732

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

ATATCTGACTTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTTCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTATATTC  >  NZ_CP009273/2102551‑2102732

ATATCTGACTTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCT                                                                                    >  SRR3722116.245352/1‑100 (MQ=60)

                                 AGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTctgtctctta                                                   >  SRR3722116.86912/1‑90 (MQ=60)

                                                       ATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCA                             >  SRR3722116.74625/1‑100 (MQ=60)

                                                          gagacagACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATAT                          <  SRR3722116.353637/93‑1 (MQ=60)

                                                                                  TCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTATATTC  <  SRR3722116.52505/100‑1 (MQ=60)

ATATCTGACTTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTTCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTATATTC  >  NZ_CP009273/2102551‑2102732

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`