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 F1 I1 R1	315	33.5	1889570	98.7%	1865005	80.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,452,220	G→A	P475S (CCT→TCT)	paaZ ←	oxepin‑CoA hydrolase/3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,452,220	0	G	A	96.2%	87.2 / NA	26	P475S (CCT→TCT)	paaZ	oxepin‑CoA hydrolase/3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase
Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (12/13); minor base T (1/0); total (13/13)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGCGGTTCGCTGCATGTAATGTTTCACCGCTCGTAAACCGCCTAATTCTTCACCGCCTCCTGCGCGACCAGGCCCACCATGTACCAGTTGTGGCAGTGGGGAGCCATGCCCGGTGGATTCTTTTGCCGACTCTTCATTGAGGATCTGAA  >  NC_000913/1452148‑1452297

cAGCGGTTCGCTGCATGTAATGTTTCACCGCTCGTAAACCGCCTAATTCTTCACCGCCTCCTGCGCGACCAGACCCACCAt                                                                       >  1:277002/1‑81 (MQ=255)

  gCGGTTCGCTGCATGTAATGTTTCACCGCTCGTAAACCGCCTAATTCTTCACCGCCTCCTGCGCGACCAGACCCACCATg                                                                      >  2:276989/1‑80 (MQ=255)

    ggTTCGCTGCATGTAATGTTTCACCGCTCGTAAACCGCCTAATTCTTCACCGCCTCCTGCGCGACCAGACCCACCATGTAc                                                                   >  2:276991/1‑81 (MQ=255)

    ggTTCGCTGCATGTAATGTTTCACCGCTCGTAAACCGCCTAATTCTTCACCGCCTCCTGCGCGACCAGACCCACCATGTAc                                                                   <  2:276955/81‑1 (MQ=255)

      ttCGCTGCATGTAATGTTTCACCGCTCGTAAACCGCCTAATTCTTCACCGCCTCCTGCGCGACCAGACCCACCATGTACCa                                                                 <  1:276956/81‑1 (MQ=255)

        cGCTGCATGTAATGTTTCACCGCTCGTAAACCGCCTAATTCTTCACCGCCTCCTGCGCGACCAGACCCACCATGTACCAg                                                                <  1:276957/80‑1 (MQ=255)

         gCTGCATGTAATGTTTCACCGCTCGTAAACCGCCTAATTCTTCACCGCCTCCTGCGCGACCAGACCCACCATGTACCAGtt                                                              >  2:276992/1‑81 (MQ=255)

         gCTGCATGTAATGTTTCACCGCTCGTAAACCGCCTAATTCTTCACCGCCTCCTGCGCGACCAGACCCACCATGTACCAGtt                                                              <  1:276959/81‑1 (MQ=255)

         gCTGCATGTAATGTTTCACCGCTCGTAAACCGCCTAATTCTTCACCGCCTCCTGCGCGACCAGACCCACCATGTACCAGt                                                               <  2:276958/80‑1 (MQ=255)

              aTGTAATGTTTCACCGCTCGTAAACCGCCTAATTCTTCACCGCCTCCTGCGCGACCAGACCCACCATGTACCAGTTGTGGc                                                         <  2:276960/81‑1 (MQ=255)

                   aTGTTTCACCGCTCGTAAACCGCCTAATTCTTCACCGCCTCCTGCGCGACCAGACCCACCATGTACCAGTTGTGGCAGTg                                                     <  1:276961/80‑1 (MQ=255)

                       ttCACCGCTCGTAAACCGCCTAATTCTTCACCGCCTCCTGCGCGACCAGTCCCACCATGTACCAGTTGTGGCAGTGGGGAg                                                >  2:277004/1‑81 (MQ=255)

                                 gTAAACCGCCTAATTCTTCACCGCCTCCTGCGCGACCAGACCCACCATGTACCAGTTGTGGCAGTGGGGAGCCATGCCCgg                                      >  1:276994/1‑81 (MQ=255)

                                             aTTCTTCACCGCCTCCTGCGCGACCAGACCCACCATGTACCAGTTGTGGCAGTGGGGAGCCATGCCCGGTGGATTCTTTTg                          >  2:276998/1‑81 (MQ=255)

                                              ttcttcACCGCCTCCTGCGCGACCAGACCCACCATGTACCAGTTGTGGCAGTGGGGAGCCATGCCCGGTGGATTCTTTTGc                         <  1:276962/81‑1 (MQ=255)

                                                     ccGCCTCCTGCGCGACCAGACCCACCATGTACCAGTTGTGGCAGTGGGGAGCCATGCCCGGTGGATTCTTTTGCCGActct                  >  1:277006/1‑81 (MQ=255)

                                                      cGCCTCCTGCGCGACCAGACCCACCATGTACCAGTTGTGGCAGTGGGGAGCCATGCCCGGTGGATTCTTTTGCCGACTCtt                 <  2:276963/81‑1 (MQ=255)

                                                       gCCTCCTGCGCGACCAGACCCACCATGTACCAGTTGTGGCAGTGGGGAGCCATGCCCGGTGGATTCTTTTGCCGACTCtt                 >  1:277001/1‑80 (MQ=255)

                                                         ctcctGCGCGACCAGACCCACCATGTACCAGTTGTGGCAGTGGGGAGCCATGCCCGGTGGATTCTTTTGCCGACTCTTCAt              >  1:277003/1‑81 (MQ=255)

                                                            ctGCGCGACCAGACCCACCATGTACCAGTTGTGGCAGTGGGGAGCCATGCCCGGTGGATTCTTTTGCCGACTCTTCATTg            <  1:276964/80‑1 (MQ=255)

                                                                gcgACCAGACCCACCATGTACCAGTTGTGGCAGTGGGGAGCCATGCCCGGTGGATTCTTTTGCCGACTCTTCATTGAGGAt       <  2:276965/81‑1 (MQ=255)

                                                                 cgACCAGACCCACCATGTACCAGTTGTGGCAGTGGGGAGCCATGCCCGGTGGATTCTTTTGCCGACTCTTCATTGAGGATc      >  2:276995/1‑81 (MQ=255)

                                                                   aCCAGACCCACCATGTACCAGTTGTGGCAGTGGGGAGCCATGCCCGGTGGATTCTTTTGCCGACTCTTCATTGAGGATCTg    <  2:276966/81‑1 (MQ=255)

                                                                    ccAGACCCACCATGTACCAGTTGTGGCAGTGGGGAGCCATGCCCGGTGGATTCTTTTGCCGACTCTTCATTGAGGATCTGa   <  1:276967/81‑1 (MQ=255)

                                                                     cAGACCCACCATGTACCAGTTGTGGCAGTGGGGAGCCATGCCCGGTGGATTCTTTTGCCGACTCTTCATTGAGGATCTGaa  >  1:276997/1‑81 (MQ=255)

                                                                     cAGACCCACCATGTACCAGTTGTGGCAGTGGGGAGCCATGCCCGGTGGATTCTTTTGCCGACTCTTCATTGAGGATCTGaa  >  2:277010/1‑81 (MQ=255)

CAGCGGTTCGCTGCATGTAATGTTTCACCGCTCGTAAACCGCCTAATTCTTCACCGCCTCCTGCGCGACCAGGCCCACCATGTACCAGTTGTGGCAGTGGGGAGCCATGCCCGGTGGATTCTTTTGCCGACTCTTCATTGAGGATCTGAA  >  NC_000913/1452148‑1452297

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A