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
A13 F20 I0 R1	91	60.0	1338914	94.3%	1262595	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,797,772	G→C	100%	R7G (CGC→GGC)	USA300HOU_1679 ←	sensor histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,797,772	0	G	C	100.0%	173.5 / ‑6.5	56	R7G (CGC→GGC)	USA300HOU_1679	sensor histidine kinase
Reads supporting (aligned to +/- strand): ref base G (0/0); major base C (23/31); minor base A (2/0); total (25/31)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AAATATATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTCT  >  CP000730/1797637‑1797909

aaataTATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCcgtggt                                                                                                                                      <  1:616093/141‑1 (MQ=255)

      atGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACt                                                                                                                                >  2:518945/1‑141 (MQ=255)

           cTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTtcatc                                                                                                                           >  1:620596/1‑141 (MQ=255)

                gtCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAACACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAAGAAAACGGATAATTGATATACTGCTTATCAATAACATTCAACAGCAGTGAAACTGcatcatacg                                                                                                                      >  2:507301/2‑138 (MQ=255)

                aTCTGTTGCTAGAGCTTGTTCGTGTTTTTCCAATAAGACAGATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATACTTAAGATCCTGCTTTTCAATATCGTTATGCCGTGGTGAAACTTGTTCGTTGt                                                                                                                      >  1:192235/1‑141 (MQ=255)

                 tCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGCTAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTCGTGAAAATTCATCATTGtt                                                                                                                     >  2:611750/1‑141 (MQ=255)

                 tCTGTTGCTAGAGCATGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAACATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGtt                                                                                                                     >  1:350104/1‑141 (MQ=255)

                  cTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTc                                                                                                                    >  1:648678/1‑141 (MQ=255)

                         tAGAGCTTGTTCGTGTTTTTATGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGCTGTAACTTTATCATTGTTCTTTAGGt                                                                                                             >  1:404415/1‑141 (MQ=255)

                           gaccTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCt                                                                                                           <  2:197941/138‑1 (MQ=255)

                                tGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCa                                                                                                      <  2:147998/141‑1 (MQ=255)

                                    cGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACGTCATCATTGTTCTTTAGGTCTTTCCAAttt                                                                                                  >  1:621445/1‑141 (MQ=255)

                                     gtttttttCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTta                                                                                                 <  2:258762/138‑1 (MQ=255)

                                              tGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAg                                                                                        >  1:13570/1‑141 (MQ=255)

                                              tGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACAGATTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAg                                                                                        >  2:238011/1‑141 (MQ=255)

                                               gATAAAACATATGTGATGGAAGCGTGAATACTAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGAGGTGAAACTTCATCATTGTCCTTTAAGTCTTTCCAATTTATAGCCTAAGc                                                                                       <  2:491474/141‑1 (MQ=255)

                                                      cATATGTGATGGAAGCGTGAATATTATTGCCTAATGTAACAAATCTGATAATTAATATACTGCTTTTTAATTACATTAAGTCCTTGTGCAGCTTCATAATTATTTTTTAGTTCTTTCCAGATTAGAGCCGAAGCCACGcac                                                                                <  2:192235/141‑1 (MQ=255)

                                                       atatGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGcaca                                                                               >  1:11037/1‑141 (MQ=255)

                                                          tgtgATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATGCTGCTTATCAATAACATTAAGCCGTGGTGAAACATCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCAACGcgcatat                                                                            >  1:25593/1‑138 (MQ=255)

                                                            tgATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACGGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCTACGCCCAGtttt                                                                          >  2:16962/1‑141 (MQ=255)

                                                                   atcttGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACCTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGt                                                                   <  2:2854/137‑1 (MQ=255)

                                                                   aGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGt                                                                   <  1:458032/141‑1 (MQ=255)

                                                                   aGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGt                                                                   <  1:186408/141‑1 (MQ=255)

                                                                   aGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGt                                                                   <  1:358965/141‑1 (MQ=255)

                                                                   aGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTGTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGt                                                                   <  1:457866/141‑1 (MQ=255)

                                                                   aGCGTGAATAATAACGCCTAATGTAACAAAACTGATTATTTATGTACTGCTTCTCCATAAGCTTAAGCCATGGTGAAACCTCATCTTTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGt                                                                   <  2:203748/141‑1 (MQ=255)

                                                                   aGCGTAAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGt                                                                   <  2:281095/141‑1 (MQ=255)

                                                                    gCGTTAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGtt                                                                  <  1:604378/141‑1 (MQ=255)

                                                                    gCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGtt                                                                  <  2:63455/141‑1 (MQ=255)

                                                                    gCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGtt                                                                  <  1:187884/141‑1 (MQ=255)

                                                                    gCGGGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATCGCCTAAGCCACGCACAGTTTTAATAAGtt                                                                  <  2:142861/141‑1 (MQ=255)

                                                                     cGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGACACTTCATCATTGTTCTTTCGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTtg                                                                 >  2:454937/1‑141 (MQ=255)

                                                                       gggataataatGCCTAATGTAACCAAACTGATAATTAATATACCGCTTATCAATAACATTAAGGCGTGGTGAAACGTCAACATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTtgtg                                                               <  1:257416/138‑1 (MQ=255)

                                                                        gAATAATAATGCCTAATGTCACAAAACTGATAATTAATATACTGCTTTTCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTGCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACGGTTTTACTACGTTGTgg                                                              >  1:305372/1‑141 (MQ=255)

                                                                           tactaatGCCTAATGTACCGAAACTGATAATTAATATTCTGCCTAACTATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAAGTTTTTCCAATTTATAGCCTAAGCCGCGCACAGTTTTAATAAGTTGTGGctt                                                           <  2:426872/138‑1 (MQ=255)

                                                                               aatGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTa                                                       >  1:117497/1‑141 (MQ=255)

                                                                                   ccTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGAt                                                   <  2:618425/141‑1 (MQ=255)

                                                                                   ccTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGAt                                                   <  1:231287/141‑1 (MQ=255)

                                                                                           aaCAAAACTGATAATTAATATACTGCTTATCAATAACATTATACAGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGTTTActttct                                           >  2:501950/1‑141 (MQ=255)

                                                                                           aaCAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTAtcttct                                           <  2:127842/141‑1 (MQ=255)

                                                                                             cAAAACTGATAATTAATATACTTCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTaa                                         <  2:603409/141‑1 (MQ=255)

                                                                                                aaCTGATAATTAATATAATGCTTATAAATAACATTAAGCCGTGGTGATACAACATCAATGTTTTTTAGGTCTATCAAATTTGTAGCCTAAGCCAAGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTATAAttt                                      >  2:191353/1‑141 (MQ=255)

                                                                                                        agtactagaCTGCTTATCAATAGCATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTa                              <  2:667379/133‑1 (MQ=255)

                                                                                                         ttaatATACTGCTTATCAATAACATTAATCCGGTGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTaa                             <  2:40412/141‑1 (MQ=255)

                                                                                                            atatACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATCAGTTGTGGCTTCTTAGGACTATCTCCTAATTTATCTCTTAAATg                          <  1:366374/141‑1 (MQ=255)

                                                                                                            atatACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATg                          >  1:470608/1‑141 (MQ=255)

                                                                                                               taCTTCTTATCAATAACATTAAGCCGTGGTGAAACTTCAAACTTGTTATTTAAGCCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACt                       <  1:217387/141‑1 (MQ=255)

                                                                                                               taCTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACt                       <  1:571748/141‑1 (MQ=255)

                                                                                                                 cTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGAGTATCTTCTAATTTATCTCTTAAATGACTGa                     >  2:352240/1‑141 (MQ=255)

                                                                                                                    cTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGatat                  <  1:238011/141‑1 (MQ=255)

                                                                                                                    cTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGatat                  <  2:403422/141‑1 (MQ=255)

                                                                                                                         cAATAACATTAAGCCGTGGTGACCGGTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTAct             >  2:474218/1‑140 (MQ=255)

                                                                                                                            tAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAGGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATca          >  1:394032/1‑141 (MQ=255)

                                                                                                                            tAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATca          <  2:404415/141‑1 (MQ=255)

                                                                                                                              aCATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATcaac        <  1:280664/141‑1 (MQ=255)

                                                                                                                                   aaGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATTTACAAttt   >  1:385272/1‑140 (MQ=255)

                                                                                                                                    aGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTGCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAGGGTGTGGCTTTTTAGGATTGCCCTCTAATTTATCTCTTAACTGACTGATATTTACATGAAGAGTTCt  >  1:254181/1‑141 (MQ=255)

AAATATATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTCT  >  CP000730/1797637‑1797909

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A