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 F1 I1 R1	778	68.7	3228504	93.4%	3015422	109.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,549,755	C→T	E106K (GAA→AAA)	malQ ←	4‑alpha‑glucanotransferase (amylomaltase)

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,549,755	0	C	T	100.0%	134.8 / NA	42	E106K (GAA→AAA)	malQ	4‑alpha‑glucanotransferase (amylomaltase)
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (19/23); total (19/23)

TAAAGCTGAACGCAGGCACCCCACAGCTTTTGTTTATTCAGCAACGCCTGCGGTTCGTAACAGCGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTCCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACATGGCCTTTGTACTGCGTTCCTTCTTCGGTGGTCAGCAGCCAGCTATATTCGCCGCTGCCCTCCACCACCATCGGCATTTTTTTGC  >  NC_000913/3549619‑3549883

taAAGCTGAACGCAGGCACCCCACAGCTTTTGTTTATTCAGCAACGCCTGCGGTTCGTAACAGCGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCGGCGTGTGATAACCTTTCg                                                                                                                                >  2:1080661/1‑139 (MQ=255)

        aaCGCAGGCACCCCACAGCTTTTGTTTATTCAGCAACGCCTGCGGTTCGTAACAGCGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTtc                                                                                                                        >  2:180616/1‑139 (MQ=255)

        aaCGCAGGCACCCCACAGCTTTTGTTTATTCAGCAACGCCTGCGGTTCGTAACAGCGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTtc                                                                                                                        >  2:486339/1‑139 (MQ=255)

              ggCACCCCACAGCTTTTGTTTATTCAGCAACGCCTGCGGTTCGTAACAGCGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGt                                                                                                                  <  1:180616/139‑1 (MQ=255)

                     cacaGCTTTTGTTTATTCAGCAACGCCTGCGGTTCGTAACAGCGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGa                                                                                                           <  1:1221656/139‑1 (MQ=255)

                             ttGTTTATTCAGCAACGCCTGCGGTTCGTAACAGCGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTg                                                                                                   >  2:735036/1‑139 (MQ=255)

                               gTTTATTCAGCAACGCCTGCGGTTCGTAACAGCGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGcc                                                                                                 <  1:1080661/139‑1 (MQ=255)

                               gTTTATTCAGCAACGCCTGCGGTTCGTAACAGCGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGcc                                                                                                 <  1:735036/139‑1 (MQ=255)

                                 ttATTCAGCAACGCCTGCGGTTCGTAACAGCGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGcccc                                                                                               <  2:1592822/139‑1 (MQ=255)

                                   aTTCAGCAACGCCTGCGGTTCGTAACAGCGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGcccccc                                                                                             <  2:1454006/139‑1 (MQ=255)

                                    ttCAGCAACGCCTGCGGTTCGTAACAGCGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCg                                                                                            >  1:1220780/1‑139 (MQ=255)

                                        gCAACGCCTGCGGTTCGTAACAGCGTTTCGGGGCGACAATCACCCGGCACTGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAGCGCTTTGCCCCCCGTTAc                                                                                        <  1:833002/139‑1 (MQ=255)

                                          aaCGCCTGCGGTTCGTAACAGCGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACAt                                                                                      <  1:1333392/139‑1 (MQ=255)

                                            cGCCTGCGGTTCGTAACAGCGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACATgg                                                                                    >  1:402153/1‑139 (MQ=255)

                                              ccTGCGGTTCGTAACAGCGTTTCGGGGCGACAAT‑ACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGc                                                                                                                           <  1:410818/97‑1 (MQ=255)

                                              ccTGCGGTTCGTAACAGCGTTTCGGGGCGACAAT‑ACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGc                                                                                                                           >  2:410818/1‑97 (MQ=255)

                                                 gCGGTTCGTAACAGCGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACATGGCCttt                                                                               >  2:725371/1‑139 (MQ=255)

                                                       cGTAACAGCGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACATgg                                                                                    <  1:447057/128‑1 (MQ=255)

                                                       cGTAACAGCGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACATgg                                                                                    >  2:447057/1‑128 (MQ=255)

                                                         tAACAGCGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACATGGCCTTTGTACTGCg                                                                       >  2:679099/1‑139 (MQ=255)

                                                          aaCAGCGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACATGGCCTTTGTACTGCGt                                                                      <  2:83311/139‑1 (MQ=255)

                                                           aCAGCGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACATGGCCTTTGTACTGCGtt                                                                     <  1:486339/139‑1 (MQ=255)

                                                            cAGCGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACATGGCCTTTGTACTGCGTTc                                                                    <  1:1242640/139‑1 (MQ=255)

                                                             aGCGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGCCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACATGGCCTTTGTACTGCGTTcc                                                                   >  2:966561/1‑139 (MQ=255)

                                                               cGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACATGGCCTTTGTACTGCGTTCctt                                                                 >  2:177539/1‑139 (MQ=255)

                                                                              aTCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACATGGCCTTTGTACTGCGTTCCTTCTTCGGTGGTcagca                                                  <  2:402153/139‑1 (MQ=255)

                                                                                cACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACATGGCCTTTGTACTGCGTTCCTTCTTCGGTGGTCagcagc                                                <  1:679099/139‑1 (MQ=255)

                                                                                cACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACATGGCCTTTGTACTGCGTTCCTTCTTCGGTGGTCagcagc                                                <  1:177539/139‑1 (MQ=255)

                                                                                            cgcgcgcTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCtt                                                                                                                         <  2:982201/54‑1 (MQ=255)

                                                                                            cgcgcgcTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCtt                                                                                                                         >  1:982201/1‑54 (MQ=255)

                                                                                                cgcTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACATGGCCTTTGTACTGCGTTCCTTCTTCGGTGGTCAGCAGCCAGCTATATTcgccgc                                <  2:1220780/139‑1 (MQ=255)

                                                                                                 gcTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACATGGCCTTTGTACTGCGTTCCTTCTTCGGTGGTCAGCAGCCAGCTATATTCGCCGCt                               <  2:354436/139‑1 (MQ=255)

                                                                                                   tggccgtcCTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACATGGCCTTTGTACTGCGTTCCTTCTTCGGTGGTCAGCAGCCAGCTATATTCGCCGCTGc                             <  1:966561/135‑1 (MQ=255)

                                                                                                           cTGGGTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACATGGCCTTTGTACTGCGTTCCTTCTTCGGTGGTCAGCAGCCAGCTATATTCGCCGCTGCCCTccacc                     >  1:1238317/1‑139 (MQ=255)

                                                                                                              ggTGAGTGTCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACATGGCCTTTGTACTGCGTTCCTTCTTCGGTGGTCAGCAGCCAGCTATATTCGCCGCTGCCCTccaccacc                  <  2:822/139‑1 (MQ=255)

                                                                                                                    tgtCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGcccccc                                                                                             >  2:1529884/1‑58 (MQ=255)

                                                                                                                    tgtCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGcccccc                                                                                             <  1:1529884/58‑1 (MQ=255)

                                                                                                                    tgtCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACATGGCCTTTGTACTGCGTTCCTTCTTCGGTGGTCAGCAGCCAGCTATATTCGCCGCTGCCCTCCACCACCATCGGc            >  2:477912/1‑139 (MQ=255)

                                                                                                                    tgtCAGCGTGTGATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACATGGCCTTTGTACTGCGTTCCTTCTTCGGTGGTCAGCAGCCAGCTATATTCGCCGCTGCCCTCCACCACCATCGGc            >  1:1095081/1‑139 (MQ=255)

                                                                                                                              tgATAACCTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACATGGCCTTTGTACTGCGTTCCTTCTTCGGTGGTCAGCAGCCAGCTATATTCGCCGCTGCCCTCCACCACCATCGGCATTTTTTTGc  >  1:744741/1‑139 (MQ=255)

                                                                                                                                    ccTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGc                                                                                                  <  2:608180/37‑1 (MQ=255)

                                                                                                                                    ccTTTCGGCAGCTTCGTCGGTAGATTGAACGCTTTGc                                                                                                  >  1:608180/1‑37 (MQ=255)

TAAAGCTGAACGCAGGCACCCCACAGCTTTTGTTTATTCAGCAACGCCTGCGGTTCGTAACAGCGTTTCGGGGCGACAATCACCCGGCAATGCGCGCGCTGGTCGTCCTGGGTGAGTGTCAGCGTGTGATAACCTTCCGGCAGCTTCGTCGGTAGATTGAACGCTTTGCCCCCCGTTACATGGCCTTTGTACTGCGTTCCTTCTTCGGTGGTCAGCAGCCAGCTATATTCGCCGCTGCCCTCCACCACCATCGGCATTTTTTTGC  >  NC_000913/3549619‑3549883

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A