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 I197 R1	189	12.7	697584	97.1%	677354	86.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,897,230	A→G	D309G (GAT→GGT)	manX →	PTS mannose transporter subunit IIAB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,897,230	0	A	G	83.3%	19.4 / 0.5	12	D309G (GAT→GGT)	manX	PTS mannose transporter subunit IIAB
Reads supporting (aligned to +/- strand): ref base A (2/0); new base G (7/3); total (9/3)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.41e-01

GTTTCGGTTGATGAAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGATCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTAAGTCTT  >  NZ_CP009273/1897145‑1897318

gTTTCGGTTGATGAAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCg                                                                                      >  2:261585/1‑90 (MQ=255)

                   atatCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATc                                                                   <  2:37143/90‑1 (MQ=255)

                             gTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCaa                                                         >  1:236159/1‑90 (MQ=255)

                                                   ggTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGATCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATtgtg                                   >  1:324858/1‑90 (MQ=255)

                                                         gAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGaaa                                                                             <  1:68400/42‑1 (MQ=255)

                                                         gAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGaaa                                                                             >  2:68400/1‑42 (MQ=255)

                                                              ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAc                        >  1:196833/1‑90 (MQ=255)

                                                              ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAc                        >  1:285270/1‑90 (MQ=255)

                                                              ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAc                        >  1:287975/1‑90 (MQ=255)

                                                              ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAc                        >  2:275663/1‑90 (MQ=255)

                                                                aaGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTc                      <  1:66143/90‑1 (MQ=255)

                                                                                    gATCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTAAGTCtt  >  2:228760/1‑90 (MQ=255)

GTTTCGGTTGATGAAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGATCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTAAGTCTT  >  NZ_CP009273/1897145‑1897318

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `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: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

GATGAAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGATCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACA  >  NZ_CP009273/1897154‑1897308

cgccatcgtcggcagcgtcagatgtgtataagagacagGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATC                                                         <  SRR3722076.69252/62‑1 (MQ=60)

          ATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAA                                               >  SRR3722076.239445/1‑100 (MQ=60)

                                GAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGATCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTG                         >  SRR3722076.329802/1‑100 (MQ=60)

                                           GTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAC              >  SRR3722076.199353/1‑100 (MQ=60)

                                           GTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAC              >  SRR3722076.289502/1‑100 (MQ=60)

                                           GTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAC              >  SRR3722076.292260/1‑100 (MQ=60)

                                                       AAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACA  <  SRR3722076.66966/100‑1 (MQ=60)

GATGAAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGATCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACA  >  NZ_CP009273/1897154‑1897308

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`