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 F191 I0 R1	49	68.0	1456600	97.2%	1415815	140.0

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%	119.4 / NA	44	R7G (CGC→GGC)	USA300HOU_1679	sensor histidine kinase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (21/23); total (21/23)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AAATATATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTC  >  CP000730/1797637‑1797908

aaataTATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCcgtgg                                                                                                                                      <  1:609182/140‑1 (MQ=255)

aaataTATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAACCcgtgg                                                                                                                                      >  1:120836/1‑140 (MQ=255)

       tGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATTTACTGCTAATCAATAACATTAAGAggcggataagat                                                                                                                               >  2:326558/1‑133 (MQ=255)

        gATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACtt                                                                                                                              >  2:69433/1‑140 (MQ=255)

         aTCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGCGGTGAAAGTtc                                                                                                                             >  1:695250/1‑140 (MQ=255)

          tCTTGCATCTGTTGCTAGAGCTTGTTCATGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTtca                                                                                                                            >  2:581562/1‑140 (MQ=255)

             tGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATCTGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGATTATCAATAACATTAAGCCGTCGTGAAACTtcatca                                                                                                                         >  2:397489/1‑140 (MQ=255)

                 tCTGTTGCTAGATCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGt                                                                                                                     <  2:404203/140‑1 (MQ=255)

                 tCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACATCATCATTGt                                                                                                                     >  1:80364/1‑140 (MQ=255)

                  cTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGtt                                                                                                                    >  2:439358/1‑140 (MQ=255)

                   tGTTGCTAGAGCTTGTTCGTG‑TTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCt                                                                                                                  >  1:215875/1‑140 (MQ=255)

                     ttGCTAGAGCTTGTTCGGGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATACCATTAAGCCGTGGTGAAACTTCTTCATTGTTCtt                                                                                                                 <  2:373633/140‑1 (MQ=255)

                          agtgCTTGTTCGTGTTTTTCTGATAAAAAATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAAATAAAATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGt                                                                                                            <  1:137311/137‑1 (MQ=255)

                          agagCTTGTTCGTGTTTTTCTGATAAAACACCAGAGATGGACAACTGAAAAATAATACATACTGTAACAAAAATAAAAATTAAAATATCACAAAAACAAAACATAAAGCCACGCTTATACTTCATCATTTTTCTTTAGGt                                                                                                            >  2:604825/1‑140 (MQ=255)

                          agagCTTGTTCATGTTTTTCTGATACGACTTGAATGATGCAGGCGTGAATAATAATGACTAATGTAACAAAACTGATAATTAATATACTGCTTATAACTCACATTAAGCCGTGGTGACACTTCATCATTGTCGTTTAgta                                                                                                            >  2:123178/1‑138 (MQ=255)

                             gcttttgcttggttttCTTATAAAACATACGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAATACTGATAATTAATATACTTCTCATCAATAATATTAAGCCGTGGTGAAACTTCATTATTGTTCTTTCGGTCtt                                                                                                         <  2:376497/128‑1 (MQ=255)

                             gCTTGTTCGTGTTTTTTTGTTTTATCTTATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTCCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCtt                                                                                                         >  2:205761/1‑140 (MQ=255)

                              cTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCttt                                                                                                        >  2:638770/1‑140 (MQ=255)

                              cTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGCGGAAAGATAATCATTGTTATGAAGGTCgtt                                                                                                        >  2:567546/1‑140 (MQ=255)

                                 gTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCAATGTTCTTTAGGTCTTTCCa                                                                                                     >  1:85764/1‑140 (MQ=255)

                                    cGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAAtt                                                                                                  >  2:129914/1‑140 (MQ=255)

                                         ttttCTGATAAATCCCATGTGTCGGAAGTGTTAATAATAATGCCTAATGTAACAAAACTGATTATTAATATTCTGCTTATCAATAACATTAATCCGTGGTGATTTTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAg                                                                                             <  2:20786/140‑1 (MQ=255)

                                         ttttCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAg                                                                                             <  1:112953/140‑1 (MQ=255)

                                            tCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAAATGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCt                                                                                          >  1:137843/1‑140 (MQ=255)

                                            tCTGATAAAACATATGTGATGGAAGCGTGAACAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATATCCt                                                                                          >  1:126117/1‑140 (MQ=255)

                                              tGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAACCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTaa                                                                                        >  1:252035/1‑140 (MQ=255)

                                                      cATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGca                                                                                <  2:268426/140‑1 (MQ=255)

                                                       atatGGGATGGGAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGcac                                                                               <  2:103226/140‑1 (MQ=255)

                                                         atGTGATTGAAGCGTGAATAATAATGCCTAATGCAACAAAACTGATAATTAATATACTGCTTATCAATCACATTAAGCCGTGGCGAAACTTCATCATCGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAg                                                                             <  2:568730/140‑1 (MQ=255)

                                                                     cGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACGTTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGtt                                                                 <  2:521767/140‑1 (MQ=255)

                                                                     cGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGtt                                                                 <  1:561728/140‑1 (MQ=255)

                                                                      gTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAATCTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTtg                                                                <  1:357540/140‑1 (MQ=255)

                                                                      gTGAATAATAATGCCTAATGTAACAAAACTGATAATTAAGATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTtg                                                                <  2:197295/140‑1 (MQ=255)

                                                                           taataatGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGct                                                           >  2:712960/1‑140 (MQ=255)

                                                                              taatGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTCCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGcttct                                                        >  2:327976/1‑140 (MQ=255)

                                                                                             cAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTa                                         <  1:265234/140‑1 (MQ=255)

                                                                                             cAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTa                                         <  1:118011/140‑1 (MQ=255)

                                                                                               aaaCTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAAt                                       <  1:132339/140‑1 (MQ=255)

                                                                                                        attaatATAATGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCtt                              >  2:468210/1‑140 (MQ=255)

                                                                                                         ttaatATACTTCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATATGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTa                             <  1:717231/140‑1 (MQ=255)

                                                                                                           aatATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTaaa                           <  1:205761/140‑1 (MQ=255)

                                                                                                                  tGCTTATCAATAACATTAAGCCGTGGTGAAATGTCATTAGTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGa                    <  2:396752/140‑1 (MQ=255)

                                                                                                                     ttATCAATAACATTAAGCCGTGGTGAAAATTCATCATTGTTCTTTAGGTCTTTCAAATTTATAGCCTACGCCACGCACAGATTTAATAAGTTCTGGCTTCTTAGGATTATCTTCTACTTTATCTCTTAAATACCTCatat                 >  2:437468/1‑140 (MQ=255)

                                                                                                                      tATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATg                <  1:224054/140‑1 (MQ=255)

                                                                                                                       aTCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGGTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGt               <  1:640071/140‑1 (MQ=255)

                                                                                                                             aaCATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTATGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATca         <  2:713394/140‑1 (MQ=255)

                                                                                                                                    aGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTc  <  1:455693/140‑1 (MQ=255)

AAATATATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTC  >  CP000730/1797637‑1797908

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