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
A15 F116 I0 R1	44	26.4	562224	96.5%	542546	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	39,378	C→T	100%	D586N (GAT→AAT)	mecA ←	penicillin binding protein 2 prime

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	39,378	0	C	T	74.1%	47.0 / 16.5	31	D586N (GAT→AAT)	mecA	penicillin binding protein 2 prime
Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (9/13); minor base A (7/1); total (16/15)
Fisher's exact test for biased strand distribution p-value = 3.95e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGCCATT  >  CP000730/39241‑39513

aaTAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATAttttc                                                                                                                                      >  2:9092/1‑141 (MQ=255)

 aTAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAATCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATAttttct                                                                                                                                     >  2:258842/1‑141 (MQ=255)

            catGTTTGGATTATCTTTATCATATGATATAAACCACAAAATTTGTCTGCCAGGTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGtttt                                                                                                                          >  2:210599/1‑141 (MQ=255)

              tGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCGTAAGATCTATAAATATTTTCTTTATGTGTtttat                                                                                                                        >  2:167520/1‑141 (MQ=255)

              tGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTtttat                                                                                                                        >  2:55175/1‑141 (MQ=255)

               gTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTtttatt                                                                                                                       <  2:236066/141‑1 (MQ=255)

                tttGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTtttattt                                                                                                                      <  1:160421/141‑1 (MQ=255)

                              aTCATATGATATAAATCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCAt                                                                                                        <  1:258842/141‑1 (MQ=255)

                                    tGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATc                                                                                                  >  1:209402/1‑141 (MQ=255)

                                              caccCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGa                                                                                        >  2:139817/1‑141 (MQ=255)

                                                                  ttCTCCTTGTTTCGTTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAaat                                                                    <  2:182785/141‑1 (MQ=255)

                                                                  ttCTCCTTGTTTCATTTTGAGTTCTGCACTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAaat                                                                    >  1:98684/1‑141 (MQ=255)

                                                                    ctcCATGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAaataa                                                                  >  1:191271/1‑141 (MQ=255)

                                                                              cATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTttctt                                                        <  2:236687/141‑1 (MQ=255)

                                                                                     aGTTCTTCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATGTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACt                                                 <  1:201240/141‑1 (MQ=255)

                                                                                     aGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACt                                                 <  1:9092/141‑1 (MQ=255)

                                                                                            cAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGtttt                                          >  1:117736/1‑141 (MQ=255)

                                                                                             aGTATCGGATTTTCTAATTAAGTTTGTATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGttttt                                         <  2:243286/141‑1 (MQ=255)

                                                                                                  cGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGGTTTATTAACGACTTGTTGCATACCATCAGTTAATAGCTTGATATTTTGTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCgcgt                                    >  2:121976/1‑141 (MQ=255)

                                                                                                    gATTTGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATCATATTTTTCTACCAAACTATGtgtaccgattct                                  >  2:122682/1‑130 (MQ=255)

                                                                                                    gATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAAAAATATTTTTCTTCCAAACTTTGTTTTTTGTGTCt                                  >  1:160396/1‑141 (MQ=255)

                                                                                                     aTTTGCCAATTAAGTTTGCATAAGAGCTATAAATATATTCTTTAGGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCtt                                 >  1:153601/1‑141 (MQ=255)

                                                                                                      tttGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGATAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTAGTTTCttt                                >  2:13083/1‑141 (MQ=255)

                                                                                                       ttGCCAATTAAGTTTGCATAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCtttt                               <  1:96872/141‑1 (MQ=255)

                                                                                                          ccAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTAAGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTAGTTTTTCGGGTCTTTtaat                            >  1:78180/1‑141 (MQ=255)

                                                                                                                   tttGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGt                   >  1:275644/1‑141 (MQ=255)

                                                                                                                      gCATAAGATCTATAAATATTTTCTTTATTTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCg                <  2:102171/141‑1 (MQ=255)

                                                                                                                        aTAAGCTCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGtt              <  2:176135/141‑1 (MQ=255)

                                                                                                                        aTAAGATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGtt              <  2:176121/141‑1 (MQ=255)

                                                                                                                        aTAAAATCTATAAATATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGtt              <  2:265136/141‑1 (MQ=255)

                                                                                                                          aagtttaataAATTTTTTCCTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTaa            <  2:78934/134‑1 (MQ=255)

                                                                                                                             aTCTATAAATATTTTCTTTATGTGTGTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTACAAATCGACTTTTTTCGTTGCTTTTAATAAGTGAGGTTCGGTAatat         >  2:268257/1‑141 (MQ=255)

                                                                                                                                    aaTATTTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGCCatt  <  1:67747/141‑1 (MQ=255)

AATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGCCATT  >  CP000730/39241‑39513

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A