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 I194 R1	197	32.2	1845014	95.2%	1756453	85.4

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%	57.9 / NA	15	coding (68/936 nt)	rfaS	LPS core biosynthesis protein RfaS
Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (7/8); total (7/8)

ATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAG  >  NZ_CP009273/3798330‑3798493

aTTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATA‑TTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGt                                                                          <  2:651835/90‑1 (MQ=255)

   atccatccCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTAc                                                                        <  2:695510/90‑1 (MQ=255)

     ccatccCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTg                                                                      <  2:332891/90‑1 (MQ=255)

        tccCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAAt                                                                   >  1:499/1‑90 (MQ=255)

        tccCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAAt                                                                   >  2:806513/1‑90 (MQ=255)

                        ttttttATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATaa                                                   <  2:177297/90‑1 (MQ=255)

                             tattaATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGc                                              <  1:371446/90‑1 (MQ=255)

                                               tttttGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTataaaata                            >  2:336252/1‑90 (MQ=255)

                                                               atTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAag            >  2:281385/1‑90 (MQ=255)

                                                                 tttttATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAagtt          <  2:55143/90‑1 (MQ=255)

                                                                  ttttATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAagtta         <  1:433470/90‑1 (MQ=255)

                                                                  ttttATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAagtta         <  2:499/90‑1 (MQ=255)

                                                                    ttATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAagttagt       >  1:466109/1‑90 (MQ=255)

                                                                    ttATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAagttagt       >  2:247014/1‑90 (MQ=255)

                                                                         ttGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAg  >  2:237794/1‑90 (MQ=255)

ATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAG  >  NZ_CP009273/3798330‑3798493

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `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

GCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAGTACATACTA  >  NZ_CP009273/3798328‑3798502

GCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAAT                                                                            >  SRR3722072.522/1‑100 (MQ=60)

                               TATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTT                                             <  SRR3722072.378050/100‑1 (MQ=60)

                                                            GTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGT                >  SRR3722072.474626/1‑100 (MQ=60)

                                                                    TTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAGTAC        <  SRR3722072.441359/100‑1 (MQ=60)

                                                                          CTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAGTACATACTA  >  SRR3722072.885293/1‑100 (MQ=60)

GCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTCCAGTACATACTA  >  NZ_CP009273/3798328‑3798502

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`