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
A5 F58 I0 R1	46	56.2	1222162	96.0%	1173275	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,391,351	G→A	26.5%	G196S (GGT→AGT)	alsT →	Amino‑acid carrier protein AlsT

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,391,351	0	G	A	26.5%	98.3 / 30.9	60	G196S (GGT→AGT)	alsT	Amino‑acid carrier protein AlsT
Reads supporting (aligned to +/- strand): ref base G (16/28); new base A (8/8); total (24/36)
Fisher's exact test for biased strand distribution p-value = 3.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

AAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTATCTTCGTTAATTGTACCGATTATGGCTATCATTTACATTGGTATGGTTTTAGTAATATTGCTATTT  >  USA300TCH1516_ALE/1391211‑1391482

aaGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAg                                                                                                                                     <  1:253950/141‑1 (MQ=255)

  ggTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGt                                                                                                                                   <  1:559075/141‑1 (MQ=255)

  ggTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAAGt                                                                                                                                   >  1:468509/1‑141 (MQ=255)

   gtgtAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGta                                                                                                                                  <  2:609321/138‑1 (MQ=255)

   gTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGta                                                                                                                                  <  2:505277/141‑1 (MQ=255)

        aaTCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAAGTattatt                                                                                                                             >  1:524066/1‑141 (MQ=255)

        aaTCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAAGTattatt                                                                                                                             >  2:286587/1‑141 (MQ=255)

        aaTCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAAGTattatt                                                                                                                             >  1:375080/1‑141 (MQ=255)

                  ggCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCg                                                                                                                   >  1:321706/1‑141 (MQ=255)

                   gggaGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAAGTATTATTTTAGCAATCGt                                                                                                                  <  2:539786/138‑1 (MQ=255)

                   gCTGGGGATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGt                                                                                                                  <  1:21902/141‑1 (MQ=255)

                     tAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAAATGCGGAGTCGTTAAATACGCAATCTAATATTAGTCCAGTAATCAGAAGTATTATTTTAGCGATCATaa                                                                                                                >  1:15537/1‑141 (MQ=255)

                          aTCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCt                                                                                                           <  2:401151/141‑1 (MQ=255)

                           tCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTAATATTTTGGCAATCGTAACAgaca                                                                                                          >  2:151309/1‑138 (MQ=255)

                             gTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCtatt                                                                                                        >  2:529649/1‑141 (MQ=255)

                                 ttGCGATTTTAATTAAAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCtattatta                                                                                                    <  1:290164/141‑1 (MQ=255)

                                   gCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCtattattaga                                                                                                  >  1:259809/1‑139 (MQ=255)

                                       ttttAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATAttgg                                                                                              >  1:273247/1‑139 (MQ=255)

                                            attacaattacaTTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACGGGTATTATTTTAGCAATCGTAACAGCTAATATTATATTTggtggt                                                                                         >  2:388101/1‑141 (MQ=255)

                                            attacaattacaTTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTggtggt                                                                                         >  2:562872/1‑141 (MQ=255)

                                              tacaattacaTTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGgtgt                                                                                       <  1:109786/141‑1 (MQ=255)

                                               tcaattacaTTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTa                                                                                      <  1:277920/140‑1 (MQ=255)

                                                caattacaTTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTAc                                                                                     >  1:315985/1‑141 (MQ=255)

                                                            catttgTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTa                                                                         >  2:32596/1‑141 (MQ=255)

                                                             atttgTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTAc                                                                        <  1:554324/141‑1 (MQ=255)

                                                              tttgTATTTACAACAGTGCAATCCAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACg                                                                       <  2:234234/141‑1 (MQ=255)

                                                              tttgTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATTTCAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACg                                                                       <  1:141567/141‑1 (MQ=255)

                                                               ttgTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGt                                                                      <  2:59949/141‑1 (MQ=255)

                                                                tgTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGtt                                                                     <  1:404045/141‑1 (MQ=255)

                                                                tgTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGtt                                                                     <  1:404054/141‑1 (MQ=255)

                                                                tgTATTTAACACAGTGCAATCCACTACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGtt                                                                     <  1:354760/141‑1 (MQ=255)

                                                                 gTATTTAACCCAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTa                                                                    <  1:18439/141‑1 (MQ=255)

                                                                 gTATTGAACACAGGGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATCAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTa                                                                    <  1:403587/141‑1 (MQ=255)

                                                                  tATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAATTACGCAATATAATATTAGTCCAGTAATCACAAGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTAt                                                                   <  2:157220/141‑1 (MQ=255)

                                                                    tgtAACAAAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAAGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTATCt                                                                 <  2:458820/139‑1 (MQ=255)

                                                                       aaCACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTATCTTCg                                                              >  1:45235/1‑141 (MQ=255)

                                                                          acaGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGAGGGTGTACGTAGTATTGCTACGTTAGCTTCGTTa                                                           >  1:409565/1‑141 (MQ=255)

                                                                                 aaTCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTATCTTCGTTAATTGTAc                                                    <  1:304489/141‑1 (MQ=255)

                                                                                   acTAATATAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTAGTGCTACGTTATCTTCGTTAATTGTACCg                                                  <  2:554969/140‑1 (MQ=255)

                                                                                       aTACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTATCTTCGTTAATTGTACCGATTa                                              >  2:539618/1‑141 (MQ=255)

                                                                                          cAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAAGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTATCTTCGTTAATTGTACCgcggagtg                                           <  2:375080/141‑8 (MQ=255)

                                                                                          cAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAAGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTATCTTCGTTAATTGTACCGATTATgg                                           <  1:286587/141‑1 (MQ=255)

                                                                                             ttGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTATCTTCGTTAATTGTCCCGATGATGGCtt                                        >  2:123958/1‑140 (MQ=255)

                                                                                              tGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTATCTTCGTTAATTGTACCGATTATGGCTAt                                       <  1:32596/141‑1 (MQ=255)

                                                                                                cGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTATCTTCGTTAATTGTACCGATTATGGCTATCa                                     <  1:190784/141‑1 (MQ=255)

                                                                                                cGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTATCTTCGTTAATTGTACCGATTATGGCTATCa                                     >  1:123888/1‑141 (MQ=255)

                                                                                                cGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAAGTATTATTTTAGCAATCGTAACAGCTATTGTTATATTTGGTGGTGTACGTAGTATTGCTACGTTATCTTCGTTAATTGTACCGATTATGGCTATCa                                     >  1:237680/1‑141 (MQ=255)

                                                                                                  gggtggTTAGAGACGCGATATAATATTGGTCCAGTAATTATAGGTTGTATTTTAGCAATCGTAACAGCTATTATTATATTGGGTGGTGTACGTAGTATTGCTACGTTGTCTTCGTTAATTGTACCGATTATGGCTATCAtt                                   <  2:271872/136‑1 (MQ=255)

                                                                                                   aGTCGTTAAATACGCAATATAATATTAGTCCAGGAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTATCTTCGTTAATTGTACCGATTATGGCTATCAttt                                  <  1:95230/141‑1 (MQ=255)

                                                                                                    gTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAAGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTATCTTCGTTAATTGTACCGATTATGGCTATCATTTa                                 >  2:353753/1‑141 (MQ=255)

                                                                                                       ggtAAATACGCAATATAATATTAGTCCAGGAATCACAAGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTATCTTCGTTAATTGTACCGATTATGGCTATCATTTACAt                              <  2:15537/139‑1 (MQ=255)

                                                                                                       gTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTATCTTCGTTAATTGTACCGATTATGGCTATCATTTACAt                              <  2:321706/141‑1 (MQ=255)

                                                                                                       gTTAAATACGAAATATAATAGTAGTCCAGTAATCACTAGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTATCTTCGTTAATTGTACCGATTATGGCTATCATTTACAt                              <  2:391591/141‑1 (MQ=255)

                                                                                                         tAAATACTCAATATAATATTAGTCCAGTAATCACAAGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTATCTTCGTTAATTGTACCGATTATGGCTATCATTTACATTg                            <  1:564848/141‑1 (MQ=255)

                                                                                                               agCAATATAATCTTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATTTTTGGTGGTGTACGTAGTATTGCTACGTTATCTTCGTTAATTGTACCGATTATGGCTATCATTTACATTGGTATgg                      <  2:427517/140‑1 (MQ=255)

                                                                                                                gCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATAACATTTGGTGGTGTACGTAGTATTGCTACGTAATCTTCGATAATTGTAACGATTATGGCTATCATGTACATTGGTATGGt                     >  2:476525/1‑141 (MQ=255)

                                                                                                                  aatataatatTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTATCTTCGTTAATTGTACCGATTATGGCTATCATTTACATTGGTATGGttt                   <  1:123958/141‑1 (MQ=255)

                                                                                                                           ttAGTCCAGTAATCACAAGTCTTATTTTAGCAATCGTAACAGCTATTTTTATATATGGTGGTGTACGTAGTATTGCTACGTTATCTTCGTTAATTGTACCGATTATGGCTATCATTTACATTGGTATGGTTTTAGTAatat          >  2:546538/1‑141 (MQ=255)

                                                                                                                            tAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTATCTTCGTTAATTGTACCGATTATGGCTATCATTTACATTGGTATGGTTTTAGTAATAtt         <  2:11403/141‑1 (MQ=255)

                                                                                                                              gTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTATCTTCGTTAATTGTACCGATTATGGCTATCATTTACATTGGTATGGTTTTAGTAATATTGc       <  2:315985/141‑1 (MQ=255)

                                                                                                                                   gTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTATCTTCGTTAATTGTACCGATTATGGCTATCATTTACATTGGTATGGTTTTAGTAATATTGCTattt  >  1:354917/1‑141 (MQ=255)

AAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCAATATAATATTAGTCCAGTAATCACAGGTATTATTTTAGCAATCGTAACAGCTATTATTATATTTGGTGGTGTACGTAGTATTGCTACGTTATCTTCGTTAATTGTACCGATTATGGCTATCATTTACATTGGTATGGTTTTAGTAATATTGCTATTT  >  USA300TCH1516_ALE/1391211‑1391482

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