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 I227 R1	223	21.3	1167702	97.0%	1132670	86.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,240,670	Δ1 bp	coding (55/441 nt)	BW25113_RS06225 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,240,667	0	G	.	78.6%	28.5 / 10.3	14	coding (52/441 nt)	BW25113_RS06225	hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (2/1); new base . (6/5); total (8/6)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.78e-01

TCCTTTTTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACCCGTT  >  NZ_CP009273/1240583‑1240754

tCCTTTTTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCg                                                                                    <  2:581634/90‑1 (MQ=255)

                                tgtgATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGaa                                                   <  2:474282/90‑1 (MQ=255)

                                  tgATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAAc                                                  >  2:226858/1‑90 (MQ=255)

                                         gAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAAAATTTAGaa                                          >  2:454150/1‑90 (MQ=255)

                                                 atatTTTAGACAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCaa                                  <  2:554196/90‑1 (MQ=255)

                                                           cAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGc                        <  1:284294/90‑1 (MQ=255)

                                                             gTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTTTTTAAAATTTAGAATTGATCAATCCTTTTGGCAg                      >  2:570934/1‑90 (MQ=255)

                                                                  cAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTaa                 <  2:405269/90‑1 (MQ=255)

                                                                    gTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGc               >  2:239202/1‑90 (MQ=255)

                                                                    gTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGc               <  2:557332/90‑1 (MQ=255)

                                                                     tCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTTAACATTTAGAATTGATCAAACCTTCTGGCAGATTAAAcc              >  2:377910/1‑90 (MQ=255)

                                                                       aGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTTGCTGCGCTTTTTTAAAATTTTGAATTGATCAATCCTTCTTGCAGATTAAACCaa            >  1:221623/1‑90 (MQ=255)

                                                                           gTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGGGCTGCGTTTTGAAAATGTAAAATAGGTAAAACCTTTTGGCAGATTGAGGCaaaaaa        >  1:357267/1‑88 (MQ=255)

                                                                                  aTGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACCCGtt  >  2:204547/1‑90 (MQ=255)

TCCTTTTTTAATTATTGTTTCGTTGTTTTTGGTGTGATTCAGAAAATAAATATTTTAGACAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACCCGTT  >  NZ_CP009273/1240583‑1240754

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 7 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

CAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACCCGTTC  >  NZ_CP009273/1240642‑1240755

CAGTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCC               <  SRR3722111.287888/100‑1 (MQ=60)

  GTAGCCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTTGCTGCGCTTTTTTAAAATTTTGAATTGATCAATCCTTCTTGCAGATTAAACCAA             >  SRR3722111.224306/1‑100 (MQ=60)

      CCAGTCAGGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGggctgcgttttgaaaatgtaaaataggtaaaaccttttggcagattgaggcaaaaaa         >  SRR3722111.362194/1‑43 (MQ=60)

             GGCGTTAAAAAT‑GGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTTTTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATAACCGTTC  >  SRR3722111.138984/1‑100 (MQ=60)

CAGTAGCCAGTCAGGCGTTAAAAATGGGGCGGATAGTGAGGCGGTTTTGGCTGCGCTTATTGAACATTTAGAATTGATCAATCCTTCTGGCAGATTAAGCCAAAATACCCGTTC  >  NZ_CP009273/1240642‑1240755

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 7 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 18 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`