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 I210 R1	226	19.6	1130256	95.4%	1078264	84.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,844,118	A→G	E342G (GAA→GGA)	sppA →	signal peptide peptidase SppA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,844,118	0	A	G	100.0%	27.1 / NA	10	E342G (GAA→GGA)	sppA	signal peptide peptidase SppA
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (3/7); total (3/7)

ACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCT  >  NZ_CP009273/1844034‑1844202

acgattacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTc                                                                                 <  1:223901/90‑1 (MQ=255)

  gattacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAg                                                                               <  2:303333/90‑1 (MQ=255)

    ttacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAggg                                                                             >  1:410948/1‑90 (MQ=255)

               aaaCGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCg                                                                  <  2:22758/90‑1 (MQ=255)

                                ggTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGca                                                 >  2:294855/1‑90 (MQ=255)

                                                  gtcTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTc                                 <  1:347697/88‑1 (MQ=255)

                                                  gtcTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTc                                 >  2:347697/1‑88 (MQ=255)

                                                             tGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCCCAAATCCGCGACGCTCGCCTTGACCCGaa                    <  1:482209/90‑1 (MQ=255)

                                                                      tATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGc           <  2:274941/90‑1 (MQ=255)

                                                                               cGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCt  <  1:156260/90‑1 (MQ=255)

ACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCT  >  NZ_CP009273/1844034‑1844202

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 20 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

ATCAGTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCTGCGTGTTAAT  >  NZ_CP009273/1844024‑1844212

ATCAGTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTC                                                                                           <  SRR3722092.96324/100‑1 (MQ=60)

    GTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGG                                                                                       >  SRR3722092.418878/1‑100 (MQ=60)

          ACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGT                                                                                 <  SRR3722092.227559/100‑1 (MQ=60)

                                                          TCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCC                                 <  SRR3722092.353973/100‑1 (MQ=60)

                                                                       TGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCCCAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCG                    <  SRR3722092.491792/100‑1 (MQ=60)

                                                                                         CGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCTGCGTGTTAAT  <  SRR3722092.158882/100‑1 (MQ=60)

                                                                                         CGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCTGCGTGTTAAT  >  SRR3722092.71381/1‑100 (MQ=60)

ATCAGTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCTGCGTGTTAAT  >  NZ_CP009273/1844024‑1844212

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 19 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`