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
A7 F123 I0 R1	46	52.8	1143652	95.1%	1087613	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	39,378	C→A	100%	D586Y (GAT→TAT)	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	A	100.0%	111.6 / NA	36	D586Y (GAT→TAT)	mecA	penicillin binding protein 2 prime
Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (23/13); total (23/13)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGCCATTA  >  CP000730/39251‑39514

atcatGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATAAATTCTTTAtgtgat                                                                                                                             >  2:185494/1‑139 (MQ=255)

     gTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTGATTTTAAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTtttatt                                                                                                                        <  1:385062/141‑1 (MQ=255)

        tGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTAc                                                                                                                     <  2:103115/141‑1 (MQ=255)

        tGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTAc                                                                                                                     <  1:91574/141‑1 (MQ=255)

             tATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACtt                                                                                                                <  2:38352/141‑1 (MQ=255)

                    aTCATATGATATAAACCACGCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGGGTTCTGCAGTGCCGGATTTGCCGATTAAGTTTGCATAAGATCTGTAAGTATATTCTTTATGTGTTTTATTTACGACTTGTTGcgt                                                                                                         >  1:427440/1‑139 (MQ=255)

                      tatttgttataACCCATCCAATTTGTTCGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTCTATTTACGACTTGTTGCATAc                                                                                                       <  2:194307/134‑1 (MQ=255)

                      cATATGATATAACCCACCCACTTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTATGAAGTACCGGATTTGCCCATTAAGGTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATAc                                                                                                       <  2:487394/141‑1 (MQ=255)

                      cATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATAc                                                                                                       >  1:266605/1‑141 (MQ=255)

                       atatGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATAcc                                                                                                      <  2:359343/141‑1 (MQ=255)

                             tataAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGt                                                                                                >  1:177048/1‑141 (MQ=255)

                             tataAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTGGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTGTATTTACGACTTGTTGCATACCATCAGt                                                                                                >  1:323190/1‑141 (MQ=255)

                                aaaCCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCCTCAGTTaa                                                                                             >  2:449723/1‑141 (MQ=255)

                                     accCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGAt                                                                                        <  2:504559/141‑1 (MQ=255)

                                        cAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGa                                                                                     >  2:421797/1‑141 (MQ=255)

                                        cAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCGTTATGTGTTTTATTTACGACTTGTTGCTTACAATAATTTTATAGATTGa                                                                                     >  2:133445/1‑141 (MQ=255)

                                                      gTTTCTCCTTGCTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAAGTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGaa                                                                       >  2:363742/1‑141 (MQ=255)

                                                           tcCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAaataat                                                                  >  2:335592/1‑141 (MQ=255)

                                                               tGTTTCATTTTGAGTTCTGCAGTCCCGGATTTGCCAATTAAGTTTGCATAAGATATATGAACATATTCTTTATGTGTTTTATTTACGGCTTGTTGAATACCGACAGTTAATAGATTGATATTTTATTTGGAAAGAAGAttt                                                              >  2:89532/1‑141 (MQ=255)

                                                                gTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATAtttt                                                             <  1:309747/141‑1 (MQ=255)

                                                                    cATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCGATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAGTAATATTTttctt                                                         >  2:419549/1‑141 (MQ=255)

                                                                               cTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGt                                              >  1:432965/1‑141 (MQ=255)

                                                                               cTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGt                                              >  1:266643/1‑141 (MQ=255)

                                                                                      aCCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCgg                                       >  1:211971/1‑140 (MQ=255)

                                                                                         ggtgttGCCAAATAAGTTTGCATTATATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTACATACCATCAGTTAATAGATTAATATTTTCTTTTCAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTc                                    <  2:554214/137‑1 (MQ=255)

                                                                                              tGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTta                               >  1:373617/1‑141 (MQ=255)

                                                                                               gCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAGCTTTGTTTTTCGTGTCTTTtaa                              >  2:550214/1‑141 (MQ=255)

                                                                                                ccAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCAAAACTTTGTTTTTCTTGTTTTTtatt                             >  2:460060/1‑139 (MQ=255)

                                                                                                            gccaaaGATCTATAAATATATTCTTTATGTGTCTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATCTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTGTTCGTGTCTTTTAATAAGTGAGGTGCg                 <  2:107144/137‑1 (MQ=255)

                                                                                                             cATAATATCTATAAATATATTCTTCATGTGTTTTATTTACGACTTGTTGCATACCATCTGTTAATAGATTGATATTTTCTTTGGAAATAATATCTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGt                <  2:357170/141‑1 (MQ=255)

                                                                                                                       ataAATATATTCTTTTTGTGTTTTATTTTCGTCTTTTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGcc      <  1:240856/141‑1 (MQ=255)

                                                                                                                       ataAATATATTCTTTATGTGTTTTGTTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGATGTGCGTTAATATTGca      >  1:534629/1‑140 (MQ=255)

                                                                                                                        taAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGCCa     >  1:340020/1‑141 (MQ=255)

                                                                                                                        taAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAAAGTTGGTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTCATATTGCCa     >  2:498569/1‑141 (MQ=255)

                                                                                                                        taAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATAACATCAGTTCATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAGCTTGTTTTTTGGTGTATTTTAAGCAGTGAGGAGCGGTAATATTGCCa     >  1:331077/1‑141 (MQ=255)

                                                                                                                          aaTATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAACAAGTGAGGTGCGGTAATATTGCCatt   >  1:158558/1‑141 (MQ=255)

                                                                                                                           atatatTGTTTATGTGTTTTATTTACGACTTGTTGCATACCTTCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTCCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGCCatta  <  1:250034/141‑1 (MQ=255)

ATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGCCATTA  >  CP000730/39251‑39514

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A