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
A13 F121 I0 R2	43	36.5	755504	99.2%	749459	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	39,246	C→T	50.4%	A630T (GCT→ACT)	mecA ←	penicillin binding protein 2 prime

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	39,246	0	C	T	50.4%	‑0.6 / 66.4	48	A630T (GCT→ACT)	mecA	penicillin binding protein 2 prime
Reads supporting (aligned to +/- strand): ref base C (13/10); new base T (9/14); total (23/25)
Fisher's exact test for biased strand distribution p-value = 3.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCT  >  CP000730/39109‑39382

gATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCcat                                                                                                                                       >  2:218643/1‑141 (MQ=255)

gATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGATCTCATATAGTTCAACATACACGTTAGCTTTTGTGGTTGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGTcat                                                                                                                                       >  1:263963/1‑141 (MQ=255)

    gCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCcatcatc                                                                                                                                   <  1:245448/141‑1 (MQ=255)

         aCTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGTGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGtt                                                                                                                              <  2:269552/141‑1 (MQ=255)

         aCTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGTCATCATCATGtt                                                                                                                              <  2:271120/141‑1 (MQ=255)

            gTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTgg                                                                                                                           <  1:217515/141‑1 (MQ=255)

               ttGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGAtt                                                                                                                        >  2:348603/1‑141 (MQ=255)

                  ttATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATc                                                                                                                     >  2:42892/1‑141 (MQ=255)

                     ttCATCTATTTCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTTATTGGCATCATCATGTTTGGATTATCttt                                                                                                                  <  2:294741/141‑1 (MQ=255)

                      tCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTa                                                                                                                 >  1:118274/1‑141 (MQ=255)

                        aTCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATc                                                                                                               >  1:207368/1‑141 (MQ=255)

                                 gTATTTTTTATTACTGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGatat                                                                                                      >  2:296247/1‑141 (MQ=255)

                                     tttttATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTTCTTTATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAac                                                                                                  <  2:173279/141‑1 (MQ=255)

                                          attaCCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCAccc                                                                                             >  1:336893/1‑141 (MQ=255)

                                                     cATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGc                                                                                  >  2:107659/1‑141 (MQ=255)

                                                     cATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGc                                                                                  >  2:163731/1‑141 (MQ=255)

                                                     cATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGc                                                                                  >  2:2606/1‑141 (MQ=255)

                                                       tataGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCa                                                                                >  1:143810/1‑141 (MQ=255)

                                                                 catACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCtt                                                                      >  1:199402/1‑141 (MQ=255)

                                                                 catACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCtt                                                                      <  1:20649/141‑1 (MQ=255)

                                                                  atACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTg                                                                     <  1:189705/141‑1 (MQ=255)

                                                                    acacTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGtt                                                                   <  2:278800/141‑1 (MQ=255)

                                                                    acacTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGtt                                                                   <  2:12962/141‑1 (MQ=255)

                                                                     cacTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGACATCATCATGTTTGGATTATCTTTATCATATGATATAAACTCCCCAATTTGTCTGCCAGTTTCTCCTTGttt                                                                  >  2:272641/1‑141 (MQ=255)

                                                                           aCCTGAGATTTTGGCATTGTAGCGAGCCATTCCTTTATCTTGTACATCGTTAACATTAATATCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCAtttt                                                            >  1:244726/1‑141 (MQ=255)

                                                                               gagaTTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGt                                                        >  1:27397/1‑141 (MQ=255)

                                                                                    tttGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGc                                                   <  1:296247/141‑1 (MQ=255)

                                                                                         cATTGTAGCTAGCCATTCCTTTATCTTGGACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTGATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTAc                                              <  1:270021/141‑1 (MQ=255)

                                                                                           ttGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCg                                            >  1:237368/1‑141 (MQ=255)

                                                                                                    gcCATTCCTTTATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCa                                   <  1:85580/141‑1 (MQ=255)

                                                                                                    gcCATTCCTTTATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCa                                   <  1:111547/141‑1 (MQ=255)

                                                                                                     ccATTCCTTTATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCaa                                  <  2:240308/141‑1 (MQ=255)

                                                                                                      cATTCCTTTATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAAt                                 <  1:323223/141‑1 (MQ=255)

                                                                                                      cATTCCTTTATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAAt                                 <  1:344458/141‑1 (MQ=255)

                                                                                                          ccTTTATCTTGTACATCTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCTATTAAg                             >  1:54161/1‑141 (MQ=255)

                                                                                                            tttATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGtt                           <  1:39108/141‑1 (MQ=255)

                                                                                                                   tGTACATCTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATaa                    >  1:151552/1‑141 (MQ=255)

                                                                                                                    gTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAg                   >  2:201651/1‑141 (MQ=255)

                                                                                                                     tACATCTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGa                  <  1:211580/141‑1 (MQ=255)

                                                                                                                     tACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGa                  >  1:132936/1‑141 (MQ=255)

                                                                                                                      aCATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGAt                 >  2:53460/1‑141 (MQ=255)

                                                                                                                       cATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATc                >  1:285613/1‑141 (MQ=255)

                                                                                                                          cTTTAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCtat             <  2:263963/141‑1 (MQ=255)

                                                                                                                           tttAACATTAATAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCtata            <  1:344916/141‑1 (MQ=255)

                                                                                                                            ttAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATaa           <  2:237463/141‑1 (MQ=255)

                                                                                                                              aaCATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAat         <  1:15854/141‑1 (MQ=255)

                                                                                                                                cATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAatat       <  1:42892/141‑1 (MQ=255)

                                                                                                                                     attgCCATCATCATGTTTGGATTATCTTTATTATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATAtattct  <  1:375913/138‑1 (MQ=255)

GATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCT  >  CP000730/39109‑39382

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A