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	195,286	T→A	100%	intergenic (‑97/‑82)	USA300HOU_0183 ← / → USA300HOU_0184	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	195,286	0	T	A	100.0%	148.7 / NA	46	intergenic (‑97/‑82)	USA300HOU_0183/USA300HOU_0184	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (30/16); total (30/16)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTTCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGAAAGAAGA  >  CP000730/195152‑195423

tttCTAGCTAAACTTGCTACGCCAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAaaaaaa                                                                                                                                      <  1:457220/141‑1 (MQ=255)

tttCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAaaaaaa                                                                                                                                      >  2:244170/1‑141 (MQ=255)

           aCTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAata                                                                                                                           >  1:308927/1‑141 (MQ=255)

              tGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTATATGTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATct                                                                                                                        >  1:250779/1‑140 (MQ=255)

               gCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCt                                                                                                                       >  1:72853/1‑141 (MQ=255)

                 tACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTg                                                                                                                     <  2:67777/141‑1 (MQ=255)

                           tCTTTATCCATTATGATAGCCCCTTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATCTTATCTAAATATTAAAAAAAATATCTTAATCTCCTTGTAATCCGATa                                                                                                           <  2:366328/141‑1 (MQ=255)

                           tCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATa                                                                                                           <  1:462972/141‑1 (MQ=255)

                            cTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCATTGTAATCCGATaa                                                                                                          >  1:79101/1‑141 (MQ=255)

                                  ccATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATta                                                                                                    <  1:205952/141‑1 (MQ=255)

                                   cATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAAttgt                                                                                                   >  1:301951/1‑139 (MQ=255)

                                       aTGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTa                                                                                               >  1:88149/1‑141 (MQ=255)

                                          aTAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAata                                                                                            >  1:405972/1‑141 (MQ=255)

                                            aGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCTATAAGAATTATAGTAAAAtt                                                                                          >  1:144474/1‑141 (MQ=255)

                                                   tatatataTGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCaa                                                                                   >  1:553480/1‑141 (MQ=255)

                                                     tatatatGTTTATTTACTTACACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATGAGAATTATAGTAATATTTTTTCAAcc                                                                                 >  1:346635/1‑141 (MQ=255)

                                                      atatatGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCa                                                                                >  1:454882/1‑141 (MQ=255)

                                                      atatagGTTTATTTAATTATACCCTAACATGATTTTTATACTCTTTAAAAATATATTTTACAGAATTTTATAAAAAAAAAAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCa                                                                                <  2:279494/141‑1 (MQ=255)

                                                        atatGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCAtt                                                                              <  1:350671/141‑1 (MQ=255)

                                                         tatGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTTTAGTAATATTTTTTCAACCATTg                                                                             >  1:225419/1‑141 (MQ=255)

                                                              ttatttaCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTtat‑a                                                                       <  1:302241/141‑1 (MQ=255)

                                                                      ttATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGATGTCt                                                               >  2:358432/1‑141 (MQ=255)

                                                                       tataCCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCtt                                                              <  1:524867/141‑1 (MQ=255)

                                                                         taCCCTAACATGATTTTTATACTCTTTGAAAATATATTATACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCttat                                                            >  1:366900/1‑141 (MQ=255)

                                                                          aCCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCttatt                                                           >  2:182304/1‑141 (MQ=255)

                                                                                aCATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGAc                                                     <  1:244170/141‑1 (MQ=255)

                                                                                aCATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAAAAACTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAA‑ATGAGGTGTAATTAGTGaa                                                     >  2:198278/1‑140 (MQ=255)

                                                                                    gATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGTGGTCTTATTAATGACattt                                                 >  1:459106/1‑140 (MQ=255)

                                                                                     aTTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTACAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACattat                                                >  1:378072/1‑141 (MQ=255)

                                                                                     aTTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACTATTGTAAT‑AGGAGGTCTTATTAATGACattat                                                >  2:540966/1‑141 (MQ=255)

                                                                                       ttttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTAttt                                              >  1:103986/1‑141 (MQ=255)

                                                                                       ttttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTAttt                                              >  1:466557/1‑141 (MQ=255)

                                                                                       ttttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTAttt                                              >  1:392436/1‑141 (MQ=255)

                                                                                       ttttATACTCTTTGAAAATATATTTTAAAGAATTTTATCTAAATATTAAAAACAATATCTTAATATTCTTGTACTCCGATAAGAATTATAGTAATATTTTTTCAACCCTTGTTGTCAGGA‑GTCTTATTAGTAACATTAttt                                              >  1:175111/1‑141 (MQ=255)

                                                                                             aCTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTATTTttatta                                        >  1:39406/1‑141 (MQ=255)

                                                                                              ctctTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATAATTTTTCAACCATGGTTAT‑AGGCGGTCTTATTAATGAAATTATTTttattat                                       >  2:221493/1‑140 (MQ=255)

                                                                                                     aaaaTATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTaa                                >  1:49647/1‑141 (MQ=255)

                                                                                                           tatTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGGATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCt                          <  1:257573/141‑1 (MQ=255)

                                                                                                              tttACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGa                       >  1:399782/1‑141 (MQ=255)

                                                                                                                    gAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGc                 <  1:153025/141‑1 (MQ=255)

                                                                                                                    aaaTTTCATCTAAATATTAAAAAAAATAGCCTAATATCGTTGGAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTCTTAT‑AGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGc                 <  1:193430/140‑1 (MQ=255)

                                                                                                                         ttATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCaa            >  2:55248/1‑141 (MQ=255)

                                                                                                                           aTCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACg          <  2:308927/141‑1 (MQ=255)

                                                                                                                            tCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTACCAATCTTGATTTTGCATCACCGa         >  1:95946/1‑141 (MQ=255)

                                                                                                                               aaaTAATAAAAAAAATATCTTTATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGAaag      <  2:18304/141‑1 (MQ=255)

                                                                                                                                 atatTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACATTCTTGATTTTGCATCAACGAaagaa    <  2:405972/141‑1 (MQ=255)

                                                                                                                                   tattAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGAAagaaga  >  2:194336/3‑141 (MQ=255)

TTTCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTAT‑AGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGAAAGAAGA  >  CP000730/195152‑195423

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A