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
A3 F34 I0 R1	41	39.6	1695432	90.3%	1530975	142.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	909,422	G→A	33.3%	A543V (GCC→GTC)	poxB ←	pyruvate oxidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	909,422	0	G	A	33.3%	32.5 / 27.4	39	A543V (GCC→GTC)	poxB	pyruvate oxidase
Reads supporting (aligned to +/- strand): ref base G (8/18); new base A (6/7); total (14/25)
Fisher's exact test for biased strand distribution p-value = 4.82e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.03e-01

ATCATGGCATGTCCTTATTATGACGGGAAATGCCACCCTTTTTACCTTAGCCAGTTTGTTTTCGCCAGTTCGATCACTTCATCACCGCGTCCGCTGATGATTGCGCGCAGCATATACAGGCTGAAACCTTTGGCCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCACCAACACCGGACCGTCGATGGAGAAGGCGCGTTGCAGGGCTTCATCAACTTCAGACGCTTTTTCTACACGGATACCCGTAA  >  NC_000913/909290‑909563

atcaTGGCATGTCCTTATTATGACGGGAAATGCCACCCTTTTTACCTTAGCCAGTTTGTTTTCGCCAGTTCGATCACTTCATCACCGCGTCCGCTGATGATTGCGCGCAGCATATACAGGCTGAAACCTTTGACCTGTTCGAg                                                                                                                                     <  2:36769/143‑1 (MQ=255)

 tcaTGGCATGTCCTTATTATGACGGGAAATGCCACCCTTTTTACCTTAGCCAGTTTGTTTTCGCCAGTTCGATCACTTCATCACCGCGTCCGCTGCTGATTGCGCGCAGCATATACAGGCTGCAACCTTTGGCCTGTTCGAGt                                                                                                                                    >  1:608358/1‑143 (MQ=255)

   aTGGCCTGTCCTTATTATGACGGGAAATGCCACCCTTTTTACCTTAGCCAGTTTGTTTTCGCCAGTTCGATCACTTCATCACCGCGTCCGCTGATGATTGCGCGCAGCATATACAGGCTGAAACCTTTGGCCTGTTCGAGttt                                                                                                                                  <  1:464263/143‑1 (MQ=255)

   aTGGCATGTCCTTATTATGACGGGAAATGCCACCCTTTTTACCTTAGCCAGTTTGTTTTCGCCAGTTCGATCACTTCATCACCGCGTCCGCTGATGATTGCGCGCAGCATATACAGGCTGAAACCTTTGGCCTGTTCGAGttt                                                                                                                                  <  1:816189/143‑1 (MQ=255)

               tattatGACGGGAAATGCCACCCTTTTTACCTTAGCCAGTTTGTTTTCGCCAGTTCGATCACTTCATCACCGCGTCCGCTGATGCTTGCGCGCAGCATATACAGGCTGACACCTTTGACCTGTTCGAGTTTGCTCTGCGGAgg                                                                                                                      >  2:419611/1‑143 (MQ=255)

                   atGACGGGAAAGGCCACCCTTTTTACCTTAGCCAGGTTGTTTTCGCCAGTTCGATCACTTCATCACCGCGTGCGCTGATGATTGCGCGCAGCATATACAGGCTGAAACCTTTGGCCTGTTCGAGTTTGATCTGCGGTGGAATg                                                                                                                  <  2:804356/143‑1 (MQ=255)

                               gccgccCTTTTTGTCGTCGCCAGTTTGCGTTCGCCAGTTCGATCACTTCATTACCGCGTTCGCTGAGGATTGCGCGCTGCATATACAGGCTGAATCCTTTGGCCTGTTCGAGTGTGATCTGCGGTGGAATGGCTAACtcttct                                                                                                      <  2:250346/143‑1 (MQ=255)

                               gCCACCCTTTTTACCTTAGCCAGTTTGTTGTCGCCAGTTCGCTCTCTTCATCACCGCGTCCGCTGATGCTTGCGCGCAGCATATACAGGCTGAAACCTTTGACCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACtcttct                                                                                                      <  2:451493/143‑1 (MQ=255)

                                 cACCCTTTTTACCTTAGCCAGTTTGTTTTCGCCAGTTCGATCACTTCATCACCGCGTCCGCTGATGATTGCGCGCAGCATATACAGGCTGAAACCTTTGACCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCttt                                                                                                    >  1:456976/1‑143 (MQ=255)

                                  aCCCTTTTTACCTTAGCCAGTTTGTTTTCGCCAGTTCGATCACTTCATCACCGCGTCCGCTGATGATTGCGCGCAGCATATACAGGCTGAAACCTTTGGCCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTg                                                                                                   <  1:43501/143‑1 (MQ=255)

                                    ccgttttACCGTAGCCAGTTTGTTTTCGCCAGTTCGATCACTTCATCACCGCGTCCGCTGATGATTGCGCGCAGTATATACAGGCTGAAACCTTTGGCCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGc                                                                                                 <  1:447475/140‑1 (MQ=255)

                                    ccTTTTTACCTTAGCCAGTTTGTTTGCACCAGTTCGCTCACTTCTTCACCGCGGCCGCTGATGATTGCGCGCAGCATTTACAGGCTGACACCTTTGGCCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGc                                                                                                 <  2:762601/143‑1 (MQ=255)

                                      tttttACCTTAGCCAGTTTGTTTTCGCCAGTTCGATCACTTCATCACCGCGTCCGCTGATGATTGCGCGCAGCATATACAGGCTGAAACCTTTGACCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGa                                                                                               <  1:491079/143‑1 (MQ=255)

                                      tttttACCTTAGCCAGGTTGTTTTCGCCAGTTCGATCACTTCATCACCGCGTCCGCTGATGATTGCGCGCAGCATATACAGGCTGAAACCTTTGACCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGa                                                                                               <  1:87220/143‑1 (MQ=255)

                                                  ccAGTTTGTTGTCGCCAGTTCGAGCACTTCATCCCCGCGTCCGCTGATGATTGCGCGCAGCATATACAGGCTGAAACCTTTGGCCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATcca                                                                                   <  1:88457/143‑1 (MQ=255)

                                                       ttgtttTCGCCAGTTCGATCACTTCATCACCGCGTCCGCTGATGATTGCGCGCAGCATATACAGGCTGAAACCTTTGGCCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCACCAac                                                                              >  2:206463/1‑143 (MQ=255)

                                                        tgtttTCGCCAGTTCGATCACTTCATCACCGCGTCCGCTGATGATTGCGCGCAGCATATACAGGCTGAAACCTTTGGCCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCACCAaca                                                                             <  1:206463/143‑1 (MQ=255)

                                                          ttttCGCCAGTTCGATCACTTCATCACCGCGTCCGCTGATGATTGCGCGCAGCATATACAGGCTGAAACCTTTGACCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCACCAACAcc                                                                           >  1:39019/1‑143 (MQ=255)

                                                          ttttCGCCAGTTCGATCACTTCATCACCGCGTCCACTGATGATTGCGCGCAGCATATACAGGCTGAAACCTTTGGCCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCCCCCACAcc                                                                           >  1:738281/1‑143 (MQ=255)

                                                                 cAGTTCGATCACTTCATCACCGCGTCCGCTGATGATTGCGCGCAGCATATACAGGCTGAAACCTTTGACCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCACCAACACCGGACCGt                                                                    >  1:419039/1‑143 (MQ=255)

                                                                        aTCACTTCATCACCGCGTCCGCTGCTGATTGCGCGCAGCATATACAGGCTGAAACCTTTGGCCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCACCAACCCCGGGCCGTCGCTGga                                                             >  1:326351/1‑143 (MQ=255)

                                                                        aTCACTTCATCACCGCGTCCGCTGATGATTGCGCGCAGCACAACAAAGCTGAATTCTTTGGCCTGTTCGATTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCACCAACACCGGACCGTCGATGga                                                             <  1:658531/143‑1 (MQ=255)

                                                                             ttCATCACCGCGTCCGCTGATGATTGCGCGCAGCATATACAGGCTGAAACCTTTGACCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCACCAACACCGGACCGTCGATGGAGAAgg                                                        >  1:638732/1‑143 (MQ=255)

                                                                             ttCATCACCGCGTCCGCTGATGATTGCGCGCAGCATATACAGGCTGAAACCTTTGACCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCACCAACACCGGACCGTCGATGGAGAAgg                                                        >  1:643124/1‑143 (MQ=255)

                                                                                      gcgTCTGCTGGTGGTTGCGCGCTGCATATACAGGCTGAAACCTTTGGCCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCACCAACACCGGACCGTCGATGGAGAAGGCGCGTTGCa                                               <  2:407381/143‑1 (MQ=255)

                                                                                      gcgTCCGCGGATGTTTGCGCGCAGCATAGGCAGGCTGGCACCTTTGGCCTGTTCGAGTTTGAGCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCACCAACACCGGACCGTCGATGGAGAAGGCGCGTTGCa                                               <  2:534760/143‑1 (MQ=255)

                                                                                       cgTCCGCTGATGATTGCGCGCAGCATATACAGGCTGACACCCTTGGCCTGTTCGAGTTTGATCTGCGGTGGAATGTCTAACTCTTCTTTGGCGACCACCACATCCACCAACACCGGACCGTCGATGGAGAAGGCGCGTTGCAg                                              <  2:423729/143‑1 (MQ=255)

                                                                                         tCCGCTGATGATTGCGCGCAGCATATACAGGCGGAAACCTTTGGCCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCACCAACACCGGACCGTCGATGGAGAAGGCGCGTTGCAggg                                            <  1:342797/143‑1 (MQ=255)

                                                                                           cGCTGAGGATTGCTCGCGTCATATACAGGGTGACGCCTTCGGCGTGTTCGAGTTTGATCTGCGGTGGAATCGCTAACTCTTCTTTGGCGACCACCACATCCACCAACACCGGACCGTCGATGGAGAAGGCGCGTTGCAGGGCt                                          <  2:608358/143‑1 (MQ=255)

                                                                                                   agtGCGCGCAGCATATACAGGCTGAAACCTTTGACCTGTTCCAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCACCAACACCGGACCGTCGATGGAGAAGGCGCGTTGCAGGGCTTCATCAAc                                  <  1:272622/141‑1 (MQ=255)

                                                                                                      gcgcgcAGCATATACAGGCTGAAACCTTTGGCCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCACCAACACCGGACCGTCGATGGAGAAGGCGCGTTGCAGGGCTTCATCAACTTc                               <  2:340802/143‑1 (MQ=255)

                                                                                                       cgcgcAGCATATACAGGCTGAAACCTTTGGCCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCACCACCACCGGACCGTCGATGGAGACGGCGCGTTGCAGGGCTTCAGCAACTTCa                              >  2:281616/1‑143 (MQ=255)

                                                                                                        gcgcAGCATATACAGGCTGAAACCTTTGACCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCACCAACACCGGACCGTCGATGGAGAAGGCGCGTTGCAGGGCTTCATCAACTTCAg                             <  1:403888/143‑1 (MQ=255)

                                                                                                               atatACAGGCTGAAACCTTTGGCCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCACCAACACCGGACCGTCGATGGAGAAGGCGCGTTGCAGGGCTTCATCACCTTCAGACGCgtt                      >  1:661581/1‑143 (MQ=255)

                                                                                                                 atgcAGGCTGGATCCTTTGGCCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCACCAACACCGGACCGTCGATGGTGAAGGCGCGTTGCAGGGCTTCATCAACTTCAGACGCtcttt                    <  2:738281/140‑1 (MQ=255)

                                                                                                                 ataCAGGCTGAAACCTTTGGCCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCACCAACACCGGACCGTCGATGGCGAAGGCGCGTTGCAGGGCTTCATCAACTTCAGACGCatttt                    >  1:100708/1‑143 (MQ=255)

                                                                                                                   accgtcTGAGACCTTTGACCTGTTCGAGGTTGATCTGCTGTGGAATGGCTAACTCGTCTTTGGCGACCGCCACATCCACCAACACCGGACCGTCGATGGAGAAGGCGCGTTGCAGGGCTTCATCAACTTCAGACGCTTTTTCt                  <  2:314268/138‑1 (MQ=255)

                                                                                                                            aaCCTTTGGCCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCACCAACACCGGACCGTCGATGGAGAAGGCGCGTTGCAGGGCTTCATCAACGTCAGACGCTTTTTCTACACGGATa         >  1:90509/1‑143 (MQ=255)

                                                                                                                                tttGGCCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCACCACCACCGGACCGTCGATGGAGAAGGCGCGTTGCAGGGCTTCATCAACTTCAGACGCTTTTTCTACACGGATACCCg     <  1:583754/143‑1 (MQ=255)

                                                                                                                                   ggCCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCACCAACACCGGACCGTCGATGGAGAAGGCGCGTTGCAGGGCTTCATCAACTTCAGACGCTTTTTCTACACGGATACCCGTaa  <  1:490806/143‑1 (MQ=255)

                                                                                                                                   ggCCTGTTCGAGTTTGATCCGCGGTGGAATGGCTAACTCTTCTTGGGCGACCACCACATCCACCAACCCCGGACCGTCGATGGAGAAGGCGCGTTGCAGGGCTTCATCAACTTCAGACGCTTTTTCTACACGGATACCCGTaa  <  2:643124/143‑1 (MQ=255)

ATCATGGCATGTCCTTATTATGACGGGAAATGCCACCCTTTTTACCTTAGCCAGTTTGTTTTCGCCAGTTCGATCACTTCATCACCGCGTCCGCTGATGATTGCGCGCAGCATATACAGGCTGAAACCTTTGGCCTGTTCGAGTTTGATCTGCGGTGGAATGGCTAACTCTTCTTTGGCGACCACCACATCCACCAACACCGGACCGTCGATGGAGAAGGCGCGTTGCAGGGCTTCATCAACTTCAGACGCTTTTTCTACACGGATACCCGTAA  >  NC_000913/909290‑909563

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A