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 F1 I2 R1	1873	183.1	9376148	98.2%	9207377	93.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,579,597	A→G	H35R (CAT→CGT)	yhhZ →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,579,597	0	A	G	100.0%	132.3 / NA	43	H35R (CAT→CGT)	yhhZ	hypothetical protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (17/26); total (17/26)

TACCTGACAGTAACGGGAGAACAACAAGGAAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCATGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTGGTTCACAGTTCCATGGTATAACATTTTGTAAAT  >  NC_000913/3579509‑3579686

tACCTGACAGTAACGGGAGAACAACAAGGAAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAg                                                                                       >  2:651608/1‑93 (MQ=255)

tACCTGACAGTAACGGGAGAACAACAAGGAAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAg                                                                                       <  1:4043961/93‑1 (MQ=255)

 aCCTGACAGTAACGGGAGAACAACAAGGAAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAgg                                                                                      >  1:1713/1‑93 (MQ=255)

  ccTGACAGTAACGGGAGAACAACAAGGAAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGa                                                                                     <  2:1252637/93‑1 (MQ=255)

     gACAGTAACGGGAGAACAACAAGGAAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGa                                                                                  >  2:3746333/1‑93 (MQ=255)

     gACAGTAACGGGAGAACAACAAGGAAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGGGAGGATGa                                                                                  >  2:1664213/1‑93 (MQ=255)

            aCGGGAGAACAACAAGGAAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATAttt                                                                           >  2:2641993/1‑93 (MQ=255)

               ggAGAACAACAAGGAAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACa                                                                        >  2:49570/1‑93 (MQ=255)

                 agaACAACAAGGAAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACAtt                                                                      <  1:3518366/93‑1 (MQ=255)

                  gaACAACAAGGAAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATtc                                                                     >  2:540550/1‑93 (MQ=255)

                     caacaaGGAAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCa                                                                  >  2:2474228/1‑93 (MQ=255)

                      aacaaGGAAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCAc                                                                 >  1:4273406/1‑93 (MQ=255)

                       acaaGGAAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCAct                                                                >  1:1269314/1‑93 (MQ=255)

                          aGGAAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCtt                                                             >  2:511292/1‑93 (MQ=255)

                             aaGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTaaa                                                          <  1:1348773/93‑1 (MQ=255)

                               gCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAaata                                                        >  2:643764/1‑93 (MQ=255)

                                cATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAaataa                                                       <  2:3427681/93‑1 (MQ=255)

                                  tctcCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAataata                                                     <  1:980427/93‑1 (MQ=255)

                                   ctcCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAatat                                                    <  2:3115838/93‑1 (MQ=255)

                                     ccGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATta                                                  <  2:4236034/93‑1 (MQ=255)

                                        cAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATtaata                                               <  1:2245/93‑1 (MQ=255)

                                         aGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATtaataa                                              <  1:3640236/93‑1 (MQ=255)

                                          ggTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTaataat                                             >  1:794035/1‑93 (MQ=255)

                                          ggTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTaataat                                             >  1:4402387/1‑93 (MQ=255)

                                                 ggACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGc                                      <  2:2787435/93‑1 (MQ=255)

                                                 ggACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGc                                      <  2:1851632/93‑1 (MQ=255)

                                                  gACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCt                                     >  2:1213704/1‑93 (MQ=255)

                                                     ttCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTgg                                  <  1:3220936/93‑1 (MQ=255)

                                                          aGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTGGTTcac                             <  2:376062/93‑1 (MQ=255)

                                                            tCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTGGTTCACAg                           <  2:847354/93‑1 (MQ=255)

                                                                  ggTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTGGTTCACAGTTCCAt                     <  2:1871827/93‑1 (MQ=255)

                                                                   gTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTGGTTCACAGTTCCATg                    <  2:1566979/93‑1 (MQ=255)

                                                                     aaTCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTGGTTCACAGTTCCATGGt                  <  1:973589/93‑1 (MQ=255)

                                                                      aTCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTGGTTCACAGTTCCATGGta                 <  2:4385089/93‑1 (MQ=255)

                                                                       tCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTGGTTCACAGTTCCATGGtat                <  1:1146154/93‑1 (MQ=255)

                                                                         gTTGGCAGAGCGGGCGTGAGGCTGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTCGTTCACAGTCCCATGGTATaa              >  2:626887/1‑93 (MQ=255)

                                                                          ttagCAGAGCGAGCGTGAGGATGAAATATTTACATACTCACTCTTAAATAATATTAATAATACGGGGCTTGGTTCACAGTTCCATGGTATAAc             <  2:4150845/90‑1 (MQ=255)

                                                                           tGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTGGTTCACAGTTCCATGGTATAACa            <  2:577240/93‑1 (MQ=255)

                                                                            ggCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTGGTTCACAGTTCCATGGTATAACAt           <  2:869039/93‑1 (MQ=255)

                                                                             gCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTGGTTCACAGTTCCATGGTATAACAtt          <  1:2627488/93‑1 (MQ=255)

                                                                              cAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTGGTTCACAGTTCCATGGTATAACAttt         <  2:328930/93‑1 (MQ=255)

                                                                               agagCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTGGTTCACAGTTCCATGGTATAACAtttt        <  2:295405/93‑1 (MQ=255)

                                                                                gagCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACAGGGCTTGGTTCACAGTTCCATGGTATAACATTTTg       >  2:3737361/1‑93 (MQ=255)

                                                                                     ggCGTGAGGATGAAATATTTACATTCTCAATCTTAAATAATATTAATAATACGGGGCTTGGTTCACAGTTCCATGGTATAACATTTTGTAaat  <  1:299567/93‑1 (MQ=255)

TACCTGACAGTAACGGGAGAACAACAAGGAAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCATGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTGGTTCACAGTTCCATGGTATAACATTTTGTAAAT  >  NC_000913/3579509‑3579686

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

TACCTGACAGTAACGGGAGAACAACAAGGAAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCATGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTGGTTCACAGTTCCATGGTATAACATTTTGTAAATTAAT  >  NC_000913/3579509‑3579690

TACCTGACAGTAACGGGAGAACAACAAGGAAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGG                                                                                          >  SRR4302535.1732/1‑94 (MQ=60)

TACCTGACAGTAACGGGAGAACAACAAGGAAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGG                                                                                          <  SRR4302535.4071648/94‑1 (MQ=60)

                 AGAACAACAAGGAAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTC                                                                         <  SRR4302535.3542807/94‑1 (MQ=60)

                     CAACAAGGAAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCAC                                                                     >  SRR4302535.4302658/1‑94 (MQ=60)

                      AACAAGGAAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACT                                                                    >  SRR4302535.1278386/1‑94 (MQ=60)

                             AAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAAT                                                             <  SRR4302535.1358406/94‑1 (MQ=60)

                                  TCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATAT                                                        <  SRR4302535.987395/94‑1 (MQ=60)

                                        CAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAA                                                  <  SRR4302535.2265/94‑1 (MQ=60)

                                         AGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAAT                                                 >  SRR4302535.799613/1‑94 (MQ=60)

                                         AGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAAT                                                 >  SRR4302535.4432515/1‑94 (MQ=60)

                                         AGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAAT                                                 <  SRR4302535.3665454/94‑1 (MQ=60)

                                                     TTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTGGT                                     <  SRR4302535.3243257/94‑1 (MQ=60)

                                                                     AATCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTGGTTCACAGTTCCATGGTA                     <  SRR4302535.980498/94‑1 (MQ=60)

                                                                       TCGTTGGCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTGGTTCACAGTTCCATGGTATA                   <  SRR4302535.1154322/94‑1 (MQ=60)

                                                                             GCAGAGCGGGCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTGGTTCACAGTTCCATGGTATAACATTT             <  SRR4302535.2646319/94‑1 (MQ=60)

                                                                                     GGCGTGAGGATGAAATATTTACATTCTCAATCTTAAATAATATTAATAATACGGGGCTTGGTTCACAGTTCCATGGTATAACATTTTGTAAATT     <  SRR4302535.301655/94‑1 (MQ=60)

                                                                                      GCGTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTGGTTCACAGTTCCATGGTATAACATTTTGTAAATTA    <  SRR4302535.2271333/94‑1 (MQ=60)

                                                                                        GTGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTGGTTCACAGTTCCATGGTATAACATTTTGTAAATTAAT  >  SRR4302535.1076393/1‑94 (MQ=60)

TACCTGACAGTAACGGGAGAACAACAAGGAAGCATCTCCGCAGGTTGTGGGACTTCTGAGTCTACAGGTAATCGTTGGCAGAGCGGGCATGAGGATGAAATATTTACATTCTCACTCTTAAATAATATTAATAATACGGGGCTTGGTTCACAGTTCCATGGTATAACATTTTGTAAATTAAT  >  NC_000913/3579509‑3579690

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`