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 F3 I95 R1	196	14.2	808436	96.0%	776098	85.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,634,151	Δ1 bp	coding (164/534 nt)	rrrQ ←	lysozyme

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,634,150	0	G	.	100.0%	40.7 / NA	11	coding (165/534 nt)	rrrQ	lysozyme
Reads supporting (aligned to +/- strand): ref base G (0/0); new base . (1/10); total (1/10)

TTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTC  >  NZ_CP009273/1634064‑1634218

ttATCCCGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACtgtgcac                                                                   <  1:244230/90‑4 (MQ=255)

    cACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCg                                                              <  2:385370/90‑1 (MQ=255)

        cTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAg                                                          >  1:383459/1‑90 (MQ=255)

          cAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGAt                                                        <  1:65664/90‑1 (MQ=255)

          cAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGAt                                                        <  2:383459/90‑1 (MQ=255)

                 gTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCat                                                 <  2:128005/90‑1 (MQ=255)

                 gTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCat                                                 <  2:378980/90‑1 (MQ=255)

                               aTTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATc                                   <  1:282813/90‑1 (MQ=255)

                                 ttttCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATcgc                                 <  2:400942/90‑1 (MQ=255)

                                           aCAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCAt                       <  2:398073/90‑1 (MQ=255)

                                                        gggAAAAACGTTTTTTCCATCCACCGCTGT‑GAACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACct          <  2:150549/90‑1 (MQ=255)

                                                                cGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTc  <  1:382123/90‑1 (MQ=255)

TTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTC  >  NZ_CP009273/1634064‑1634218

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 27 ≤` `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

CCTTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTA  >  NZ_CP009273/1634062‑1634238

CCTTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAG                                                                              >  SRR3722235.388987/1‑100 (MQ=60)

  TTATCCCGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGAT                                                                            <  SRR3722235.247349/100‑1 (MQ=60)

            CAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATG                                                                  <  SRR3722235.66411/100‑1 (MQ=60)

                                 ATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCC                                             <  SRR3722235.286697/100‑1 (MQ=60)

                                                                  CGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAAC            <  SRR3722235.387629/100‑1 (MQ=60)

                                                                            ATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTA  >  SRR3722235.9437/1‑100 (MQ=60)

CCTTATCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTA  >  NZ_CP009273/1634062‑1634238

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`