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 I211 R1	223	18.0	1007644	96.3%	970361	85.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,798,416	(T)_8→7	coding (61/936 nt)	rfaS ←	LPS core biosynthesis protein RfaS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,798,409	0	T	.	100.0%	50.7 / NA	13	coding (68/936 nt)	rfaS	LPS core biosynthesis protein RfaS
Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (7/6); total (7/6)

ATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAG  >  NZ_CP009273/3798333‑3798493

atccatccCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTAc                                                                        >  2:439471/1‑90 (MQ=255)

    atccCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATA‑TTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAAt                                                                   <  1:316130/90‑1 (MQ=255)

     tccCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGCAC‑TTTTTTTCAGGTACTGAAt                                                                   >  1:68054/1‑90 (MQ=255)

        cTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTTTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCAt                                                                >  1:288061/1‑90 (MQ=255)

                                       atatTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTtata                                 <  1:350713/90‑1 (MQ=255)

                                              tttGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTataaaataaa                          >  1:34439/1‑90 (MQ=255)

                                                tGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAaataaata                        <  1:30282/90‑1 (MQ=255)

                                                       gttATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCataa                 >  2:397458/1‑90 (MQ=255)

                                                          atatTTTTTATCTTGTAC‑TTTTTTTCAGGTTCTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCAtaataa              <  2:288061/90‑1 (MQ=255)

                                                          atatTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCAtaataa              <  2:243727/90‑1 (MQ=255)

                                                              tttttATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAagtt          >  2:390847/1‑90 (MQ=255)

                                                                    tCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTcc    <  1:301961/90‑1 (MQ=255)

                                                                      ttGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAg  >  2:176504/1‑90 (MQ=255)

ATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAG  >  NZ_CP009273/3798333‑3798493

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 34 ≤` `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

GCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAGTACATACT  >  NZ_CP009273/3798328‑3798501

GCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGCAC‑TTTTTTTCAGGTACTGAAT                                                                           >  SRR3722094.69010/1‑100 (MQ=60)

   TTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTTTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCAT                                                                        >  SRR3722094.292390/1‑100 (MQ=60)

         ATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATA‑TTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAAT                                                                 <  SRR3722094.321154/100‑1 (MQ=60)

                                         GTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAA                                  >  SRR3722094.34923/1‑100 (MQ=60)

                                            ATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAG                               <  SRR3722094.356565/100‑1 (MQ=60)

                                                     TGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAA                      <  SRR3722094.30721/100‑1 (MQ=60)

                                                                         TCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAGTACATACT  <  SRR3722094.306618/100‑1 (MQ=60)

GCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAGTACATACT  >  NZ_CP009273/3798328‑3798501

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`