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
A9 F59 I0 R1	41	42.9	928050	95.2%	883503	140.9

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%	152.7 / NA	44	intergenic (‑97/‑82)	USA300HOU_0183/USA300HOU_0184	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (23/21); total (23/21)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGAAAGAAG  >  CP000730/195153‑195422

ttCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTaaaaaaaa                                                                                                                                   <  1:365935/141‑1 (MQ=255)

          aCTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAata                                                                                                                         >  1:369607/1‑141 (MQ=255)

           cTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAatat                                                                                                                        >  1:423818/1‑141 (MQ=255)

              gCTACGACAGATTCTTTATCTATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAACATATCTTAATATCCt                                                                                                                     <  1:341728/141‑1 (MQ=255)

                  cGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTa                                                                                                                 >  1:196162/1‑141 (MQ=255)

                       gATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCg                                                                                                            >  1:427416/1‑141 (MQ=255)

                       gATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCg                                                                                                            >  2:203702/1‑141 (MQ=255)

                            tttATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTCTACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATTTCTTAATATCCTTTTAATCCgcaaaa                                                                                                       >  2:271464/1‑136 (MQ=255)

                                     aaTGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGt                                                                                              <  1:86643/141‑1 (MQ=255)

                                      aTGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTa                                                                                             >  1:443273/1‑141 (MQ=255)

                                       tGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTaa                                                                                            >  1:116728/1‑141 (MQ=255)

                                               cccTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATAtttttt                                                                                    >  2:311212/1‑141 (MQ=255)

                                                ccTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTGTTATTTTTTc                                                                                   <  1:338763/141‑1 (MQ=255)

                                                  aatatatatatatAATAACTTAAACCCTAACATGATTTTTATAATCTTTAAAAATATATTTTACTGTAATTTATAAAAAAAAAAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCaa                                                                                 <  2:24828/140‑1 (MQ=255)

                                                    tatatatGTTTATTTACTTATACCCTAACATGATTTTTTTACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAAcc                                                                               <  1:269419/141‑1 (MQ=255)

                                                    tatacatGCTTATTTACTTATACCCTAACATGATTTTTATCCTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAAcc                                                                               <  1:155/141‑1 (MQ=255)

                                                     atatatGTTTATTTACTTATACCCTAACATGATCTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATAtttttttttttt                                                                              >  2:449508/1‑135 (MQ=255)

                                                           tgttttttaCTTATACCCTAATATGATTTTTATACCCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTta                                                                        <  1:153300/136‑1 (MQ=255)

                                                            tttagttaCTTATCCCCTAACATGATTTTTATACTCTTTGCAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTtat                                                                       <  1:353397/141‑1 (MQ=255)

                                                              tatttaCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTCATCCGTTAAGAATTATAGTAATTTTTTTTGAACCTTTGGTGTag                                                                     >  1:203219/1‑141 (MQ=255)

                                                              tatttaCTTATACCCTAACATGATTTTTATACTCTTTGAAAATAGATGTTAAAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATag                                                                     >  1:203204/1‑141 (MQ=255)

                                                                tttaCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATagga                                                                   >  1:144208/1‑141 (MQ=255)

                                                                     ttATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTTTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGACt                                                              >  2:128804/1‑141 (MQ=255)

                                                                     ataaaCCCTAACATCATTTTTATAGTCTTTGAAAATATATTTTACAGAATTTTATAAAAAAAAAAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCt                                                              <  2:288991/137‑1 (MQ=255)

                                                                         aCCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCttatt                                                          >  1:75822/1‑141 (MQ=255)

                                                                              aaCATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTACATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATAGTTATAGATGGGCTTATTAAtaa                                                     >  1:271320/1‑139 (MQ=255)

                                                                              aaCATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTta                                                                        <  1:118427/122‑1 (MQ=255)

                                                                              aaCATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTta                                                                        >  2:118427/1‑122 (MQ=255)

                                                                              aaCATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCGAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTTAACCATTGTTATATGAGGTCTTATTAATGa                                                     >  1:243134/1‑141 (MQ=255)

                                                                               aCATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGAc                                                    >  1:142854/1‑141 (MQ=255)

                                                                                taTGATTTTTATACTCTTGAAAAATATATTTCACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACa                                                   <  1:376240/140‑1 (MQ=255)

                                                                                cATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACa                                                   >  2:133079/1‑141 (MQ=255)

                                                                                     tttttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACattatt                                              <  2:427416/141‑1 (MQ=255)

                                                                                        ttATAATCCTTAAAAAAATATTTGACAGAATTGTATCAAAATATAAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTAAAGTAATATGTCTACAACCATTATAATAGGAGGTCTTATTAATTACATTAttttt                                           <  2:149947/141‑1 (MQ=255)

                                                                                          ataCTCTTTGAAAATATATTATACAGAATTTTATCTAAATATTAAAAAAAATATCTTAGTATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAGTGACATTATTTttat                                         >  1:279584/1‑141 (MQ=255)

                                                                                                tttGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAg                                   <  1:203702/141‑1 (MQ=255)

                                                                                                tttGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATCATTTTTATTAGAAg                                   <  2:313326/141‑1 (MQ=255)

                                                                                                tttGAAAATATATTTTACAGAATTTTATCAAAAAATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAg                                   <  2:11486/141‑1 (MQ=255)

                                                                                                     aaaTATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAAc                              <  2:116728/141‑1 (MQ=255)

                                                                                                       atatatTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACaa                            <  1:385545/141‑1 (MQ=255)

                                                                                                               tACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGAtt                    <  1:387760/141‑1 (MQ=255)

                                                                                                                     aTTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCAt              >  2:415386/1‑141 (MQ=255)

                                                                                                                          aTCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACg         <  1:195079/141‑1 (MQ=255)

                                                                                                                               aaTATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGAaaga    >  2:453730/1‑141 (MQ=255)

                                                                                                                                 tatTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGAaagaag  <  2:203204/141‑1 (MQ=255)

TTCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGAAAGAAG  >  CP000730/195153‑195422

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