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
A1 F2 I199 R1	220	57.5	3163680	97.0%	3068769	86.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,576,634	A→G	R79R (CGA→CGG)	BW25113_RS17825 →	YrhA family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,576,634	0	A	G	100.0%	102.1 / NA	32	R79R (CGA→CGG)	BW25113_RS17825	YrhA family protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (22/10); total (22/10)

ATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAA  >  NZ_CP009273/3576549‑3576719

aTGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGgttat                                                                                   >  2:537018/1‑90 (MQ=255)

aTGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGgttat                                                                                   <  2:1566306/90‑1 (MQ=255)

  gAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTAttt                                                                                 >  1:146810/1‑90 (MQ=255)

     gTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGc                                                                              >  1:683298/1‑90 (MQ=255)

      ttAGTATTCTTTTTAAGAATCATCCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGcc                                                                             <  1:609453/90‑1 (MQ=255)

       tAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCct                                                                            >  2:690608/1‑90 (MQ=255)

       tAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCct                                                                            >  1:1414362/1‑90 (MQ=255)

       tAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCct                                                                            >  1:616864/1‑90 (MQ=255)

       tAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCct                                                                            >  2:511649/1‑90 (MQ=255)

       tAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCct                                                                            >  2:1044623/1‑90 (MQ=255)

           aTTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCg                                                                        <  2:1051980/90‑1 (MQ=255)

               tttttAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTc                                                                    >  1:1113014/1‑90 (MQ=255)

                        aTCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCtt                                                           >  2:861142/1‑90 (MQ=255)

                        aTCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCtt                                                           >  2:696937/1‑90 (MQ=255)

                        aTCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCtt                                                           >  2:260248/1‑90 (MQ=255)

                        aTCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCtt                                                           >  2:1006368/1‑90 (MQ=255)

                                 aTTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTaaaa                                                  <  2:1080087/90‑1 (MQ=255)

                                    aTCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAAcc                                               >  2:708036/1‑90 (MQ=255)

                                      cTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCtt                                             >  2:1242378/1‑90 (MQ=255)

                                       ttACTTTTTTAAGAGCAATGGATGGATTGGAAGTTAATGGATTACGGTTATTTAGTTTCTCGATTGCAGAATCTTCTGTTAAAAAACttt                                            >  1:944676/1‑90 (MQ=255)

                                         aCTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCttttt                                          <  2:1388952/90‑1 (MQ=255)

                                          ttttttgAAAAGCCGTGGATTGATTCGGGGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAAACTTCAGTTAAAAACCTTTTTg                                         >  1:791417/2‑90 (MQ=255)

                                            tttttAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGcc                                       <  2:661469/90‑1 (MQ=255)

                                              tttAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGt                                     >  1:1195708/1‑90 (MQ=255)

                                                             tggatTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAg                      >  2:1167973/1‑90 (MQ=255)

                                                              ggatTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGa                     <  2:363181/90‑1 (MQ=255)

                                                                     aaGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAatg              <  1:710653/90‑1 (MQ=255)

                                                                         tAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAAtgatga          >  2:517562/1‑90 (MQ=255)

                                                                           aTGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGAtt        <  1:782283/90‑1 (MQ=255)

                                                                           aTGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGAtt        >  1:721661/1‑90 (MQ=255)

                                                                               aTTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCAt    >  2:48447/1‑90 (MQ=255)

                                                                                ttACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATa   <  2:1133852/90‑1 (MQ=255)

                                                                                ttACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATa   <  1:1167973/90‑1 (MQ=255)

                                                                                 tACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATaa  >  2:1286313/1‑90 (MQ=255)

ATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAA  >  NZ_CP009273/3576549‑3576719

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 24 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

GTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTAC  >  NZ_CP009273/3576541‑3576731

GTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTT                                                                                             <  SRR3722078.1218450/100‑1 (MQ=60)

GTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTT                                                                                             >  SRR3722078.148518/1‑100 (MQ=60)

  TATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAG                                                                                           <  SRR3722078.1378821/100‑1 (MQ=60)

   ATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGC                                                                                          >  SRR3722078.691280/1‑100 (MQ=60)

    TGTAATGAAGTTAGTATTCTTTTAAAGAATCTACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCC                                                                                         <  SRR3722078.224659/100‑1 (MQ=60)

     GTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCT                                                                                        >  SRR3722078.1437328/1‑100 (MQ=60)

     GTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCT                                                                                        >  SRR3722078.623979/1‑100 (MQ=60)

             GTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTC                                                                                >  SRR3722078.1130009/1‑100 (MQ=60)

              TTAGTATTCTTTTTAAGAATCATCCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCC                                                                               <  SRR3722078.616491/100‑1 (MQ=60)

                                     NCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTGGAAGTTAATGGATTACGGTTATTTAGTTTCTCGATTGCAGAATCTTCTGTTAAAAAACTTT                                                        >  SRR3722078.957867/1‑100 (MQ=60)

                                        GATTATCTTATTTTTTGAAAAGCCGTGGATTGATTCGGGGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAAACTTCAGTTAAAAACCTTTTTG                                                     >  SRR3722078.801779/1‑100 (MQ=54)

                                            ATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGT                                                 >  SRR3722078.1214460/1‑100 (MQ=60)

                                                                         TTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATT                    >  SRR3722078.730606/1‑100 (MQ=60)

                                                                             AAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCAT                <  SRR3722078.719327/100‑1 (MQ=60)

                                                                                   ATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCC          <  SRR3722078.792464/100‑1 (MQ=60)

                                                                                     GGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTG        >  SRR3722078.629632/1‑100 (MQ=60)

                                                                                        TTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATC     <  SRR3722078.1186116/100‑1 (MQ=60)

                                                                                           CGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTAC  >  SRR3722078.535575/1‑100 (MQ=60)

GTTATGTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTAC  >  NZ_CP009273/3576541‑3576731

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`