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	2,470,111	G→A	54.9%	S575L (TCA→TTA)	USA300HOU_2333 ←	MFS family major facilitator transporter, multidrug:cation symporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,470,111	0	G	A	54.9%	3.4 / 64.1	49	S575L (TCA→TTA)	USA300HOU_2333	MFS family major facilitator transporter, multidrug:cation symporter
Reads supporting (aligned to +/- strand): ref base G (13/9); new base A (9/18); total (22/27)
Fisher's exact test for biased strand distribution p-value = 8.95e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.90e-01

AATAAACATAAAATTAAGGCGATGATGCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTACCTATAGAGCCTGCTAATTG  >  CP000730/2469976‑2470247

aaTAAACATAAAATTAAGGCGATGATGCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACCCTTTCATTTCGCCTTCTTGTCCGCCATATTGTAATGCt                                                                                                                                     >  2:272344/1‑141 (MQ=255)

       agaagaTTAAGGCGATGATGCTAAATAGCGTTGCAACTATAAGTGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCAt                                                                                                                              <  2:339771/136‑1 (MQ=255)

        tAAAATTAAGGCGATGATGCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATg                                                                                                                             <  1:551591/141‑1 (MQ=255)

         aaaaTTAAGGCGATGATGCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGc                                                                                                                            <  2:513859/141‑1 (MQ=255)

              tAAGTCGATGATGCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATg                                                                                                                       <  1:29723/141‑1 (MQ=255)

               aaGGCGATGATGCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCGTTGCGCCGTCTTGTCCGACATCTTGTGCTGCTCATTCACGCATCTgc                                                                                                                      >  2:195574/1‑140 (MQ=255)

                 ggCGATGATGCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATc                                                                                                                    >  1:66759/1‑141 (MQ=255)

                       gatgCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGtca                                                                                                              >  2:198864/1‑139 (MQ=255)

                       gatgCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAAACGTTGCCCGTATATTTCCAAATTGTAGTCATACTTTCCTGGCGCCTTCTTGTCCGCCGGATAGTAATGCTAAGTCATTCATATGATCTTGtcc                                                                                                              >  2:331575/1‑139 (MQ=255)

                            tAAATATCGTTGTAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAATTTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATAGTGATGCTAATTCATGCATATGATCTTGTACAACAg                                                                                                         <  1:394979/141‑1 (MQ=255)

                             aaaTATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAgg                                                                                                        <  1:237198/141‑1 (MQ=255)

                                   cGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGt                                                                                                  <  2:382399/141‑1 (MQ=255)

                                        cAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTAt                                                                                             <  2:387198/141‑1 (MQ=255)

                                              taAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAAct                                                                                       >  2:358967/1‑141 (MQ=255)

                                                   tcatcatTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTcc                                                                                  <  1:516105/140‑1 (MQ=255)

                                                   gCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGACTTCTTGTCCGCCATATTGTAATGCTAATTCATGTATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTcc                                                                                  <  1:384675/141‑1 (MQ=255)

                                                          tAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAg                                                                           >  1:480306/1‑141 (MQ=255)

                                                            aTACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCt                                                                         >  2:368036/1‑141 (MQ=255)

                                                            aTACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCt                                                                         <  1:506429/141‑1 (MQ=255)

                                                             tACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAATACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTg                                                                        <  1:26866/141‑1 (MQ=255)

                                                                         ttGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTtgtg                                                            >  1:207828/1‑141 (MQ=255)

                                                                             tAGTTTATTTACAAATTGTATTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGt                                                        <  2:142676/141‑1 (MQ=255)

                                                                                tttatttaCAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAATAGCTGATAAGTGTTGTGTTGTTtg                                                     >  1:353249/1‑141 (MQ=255)

                                                                                tttatttaCAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTtg                                                     >  2:356245/1‑141 (MQ=255)

                                                                                  tatttaCAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTtgtg                                                   <  1:53272/141‑1 (MQ=255)

                                                                                         aaaTTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCAt                                            >  1:496209/1‑141 (MQ=255)

                                                                                         aaaTTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCAt                                            >  2:181670/1‑141 (MQ=255)

                                                                                           aTTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTa                                          <  2:325252/141‑1 (MQ=255)

                                                                                                  taACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTTTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTTTCTAGTTTGTGTTGTCATTTCAATAAc                                   >  2:112295/1‑141 (MQ=255)

                                                                                                  taACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCCTTACAGTagc                                   >  1:220603/1‑139 (MQ=255)

                                                                                                   aaCACTTTCATTGGCCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACt                                  <  2:217970/141‑1 (MQ=255)

                                                                                                      ccTTTCATTGCGCCTTCTTGTCCGCCATATTTTAATGCTTATTTATGCATAAGTACTTGTACAACAGGATTCGTATTATTTAACTCTTCCTCAAAAGCTGATTAGTGTTTTTTAGTTTGTGTTGTCATTACAGTATCTAAg                               <  2:253118/140‑1 (MQ=255)

                                                                                                       cTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGa                              <  1:160335/141‑1 (MQ=255)

                                                                                                       cTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGa                              >  1:175593/1‑141 (MQ=255)

                                                                                                       cTTTCATTGCGCCTTCTTGGCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGa                              <  1:192173/141‑1 (MQ=255)

                                                                                                        tttCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAACGCGGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGAt                             <  1:323265/141‑1 (MQ=255)

                                                                                                            aTTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGGTAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCt                         >  1:482136/1‑141 (MQ=255)

                                                                                                              tGCCCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTGCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGt                       <  1:426764/141‑1 (MQ=255)

                                                                                                               gcgcCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTa                      >  1:567504/1‑141 (MQ=255)

                                                                                                                 gcCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTAcc                    >  2:523831/1‑141 (MQ=255)

                                                                                                                 gcCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGATTTATCTAACTCTTCCCCAAAAGCAGATCAGTGTTGTGTGGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTAcc                    >  2:197433/1‑141 (MQ=255)

                                                                                                                 gcCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTAcc                    <  1:368036/141‑1 (MQ=255)

                                                                                                                    ttcttGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTACCtat                 <  1:67343/141‑1 (MQ=255)

                                                                                                                        tGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTGGTAAAACAGGATTCGTTTTATCTAACTCTTACCCAAAAGCTGATAAGTGTTCTGTAGTTTGTGTTGTCATTACAGTAACTAAGAGTGCTGTAACTATagag             >  2:243833/1‑141 (MQ=255)

                                                                                                                           ccGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTACCTATAGAGCCt          <  2:362767/141‑1 (MQ=255)

                                                                                                                                atatTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTACCTATAGAGCCTGCTaa     <  2:4604/141‑1 (MQ=255)

                                                                                                                                 tatTGTAATGCTAATTGCTGCATTTGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTACCTATAGAGCCTGCTAAt    <  1:413669/141‑1 (MQ=255)

                                                                                                                                 tatTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTTTTCTCATTACAGTAACTAAGATTGCTGTACCTATAGAGCCTGCTAAt    <  1:413827/141‑1 (MQ=255)

                                                                                                                                   ttGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTACTGTACCTATAGAGCCTACTGATTg  >  2:117580/1‑141 (MQ=255)

AATAAACATAAAATTAAGGCGATGATGCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTACCTATAGAGCCTGCTAATTG  >  CP000730/2469976‑2470247

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