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
A11 F1 I1 R1	757	76.1	3598070	93.4%	3360597	108.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,099,679	C→T	L14F (CTC→TTC)	ycdY →	redox enzyme maturation protein (REMP) chaperone for YcdX

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,099,679	0	C	T	98.5%	205.8 / NA	65	L14F (CTC→TTC)	ycdY	redox enzyme maturation protein (REMP) chaperone for YcdX
Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (36/28); minor base G (0/1); total (36/29)
Fisher's exact test for biased strand distribution p-value = 4.46e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AACTTCCTTGAATCTCGCGGTATGGCACCGATTGCGGAATTTGCAGACCTTTAATTACTAGTAATGGAAATATATTAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGCTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAGTTGCTGACACGTTTGCAGAAAAGCTGTGATATGACG  >  NC_000913/1099563‑1099813

aaCTTCCTTGAATCTCGCGGTATGGCACCGATTGCGGAATTTGCAGACCTTTAATTACTAGTAATGGAAATATATTAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGa                                                                                                                  <  1:23567/139‑1 (MQ=255)

aaCTTCCTTGAATCTCGCGGTATGGCACCGATTGCGGAATTTGCAGACCTTTAATTACTAGTAATGGAAATATATTAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGa                                                                                                                  <  2:266518/139‑1 (MQ=255)

       ttGAATCTCGCGGTATGGCACCGATTGCGGAATTTGCAGACCTTTAATTACTAGTAATGGAAATATATTAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTa                                                                                                           >  2:443691/1‑139 (MQ=255)

             ctcGCGGTATGGCACCGATTGCGGAATTTGCAGACCTTTAATTACTAGTAATGGAAATATATTAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTg                                                                                                     <  1:151583/139‑1 (MQ=255)

                    tATGGCACCGATTGCGGAATTTGCAGACCTTTAATTACTAGTAATGGAAATATATTAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACcaca                                                                                                                     <  1:502179/116‑1 (MQ=255)

                    tATGGCACCGATTGCGGAATTTGCAGACCTTTAATTACTAGTAATGGAAATATATTAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACcaca                                                                                                                     >  2:502179/1‑116 (MQ=255)

                      tGGCACCGATTGCGGAATTTGCAGACCTTTAATTACTAGTAATGGAAATATATTAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGttt                                                                                            >  2:1352005/1‑139 (MQ=255)

                         cACCGATTGCGGAATTTGCAGACCTTTAATTACTAGTAATGGAAATATATTAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTAcc                                                                                         >  1:239611/1‑139 (MQ=255)

                            cGATTGCGGAATTTGCAGACCTTTAATTACTAGTAATGGAAATATATTAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACcaca                                                                                                                     <  1:1560273/108‑1 (MQ=255)

                            cGATTGCGGAATTTGCAGACCTTTAATTACTAGTAATGGAAATATATTAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACcaca                                                                                                                     >  2:1560273/1‑108 (MQ=255)

                              aTTGCGGAATTTGCAGACCTTTAATTACTAGTAATGGAAATATATTAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACcaca                                                                                                                     >  1:1531242/1‑106 (MQ=255)

                              aTTGCGGAATTTGCAGACCTTTAATTACTAGTAATGGAAATATATTAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACcaca                                                                                                                     <  2:1531242/106‑1 (MQ=255)

                              aTTGCGGAATTTGCAGACCTTTAATTACTAGTAATGGAAATATATTAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGAt                                                                                    >  1:296348/1‑139 (MQ=255)

                                  cGGAATTTGCAGACCTTTAATTACTAGTAATGGAAATATATTAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCaa                                                                                                                          <  2:1724480/97‑1 (MQ=255)

                                  cGGAATTTGCAGACCTTTAATTACTAGTAATGGAAATATATTAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCaa                                                                                                                          >  1:1724480/1‑97 (MQ=255)

                                        ttGCAGACCTTTAATTACTAGTAATGGAAATATATTAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAgggg                                                                          <  2:239611/139‑1 (MQ=255)

                                               ccTTTAATTACTAGTAATGGAAATATATTAATGAACGAGTGTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTgg                                                                   >  2:179815/1‑139 (MQ=255)

                                                 tttAATTACTAGTAATGGAAATATATTAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCt                                                                 >  2:1781868/1‑139 (MQ=255)

                                                      ttACTAGTAATGGAAATATATTAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGaa                                                            <  1:443691/139‑1 (MQ=255)

                                                          tAGTAATGGAAATATATTAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTgg                                                        >  2:1648929/1‑139 (MQ=255)

                                                                         atTAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGAt                                         <  1:1352005/139‑1 (MQ=255)

                                                                           tAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACcaca                                                                                                                     >  1:353165/1‑61 (MQ=255)

                                                                           tAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACcaca                                                                                                                     <  2:353165/61‑1 (MQ=255)

                                                                           tAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGa                                       >  1:957695/1‑139 (MQ=255)

                                                                            aaTGAACGAGTTTTCTATGCTCTGTCGTGTGCTGGGTTCGGTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAg                                      <  1:179815/139‑1 (MQ=255)

                                                                            aaTGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGAGAACTGGCCACTGGAGCAGGATGAg                                      >  2:1160704/1‑139 (MQ=255)

                                                                             aTGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAGt                                     >  1:1404864/1‑139 (MQ=255)

                                                                                aaCGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAGTTGc                                  >  1:1459330/1‑139 (MQ=255)

                                                                                         tCTATCCTCTGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAGTTGCTGACACGtt                         <  2:1459330/139‑1 (MQ=255)

                                                                                                tctGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACcaca                                                                                                                     <  1:25748/40‑1 (MQ=255)

                                                                                                tctGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACcaca                                                                                                                     >  2:25748/1‑40 (MQ=255)

                                                                                                  tGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGaa                                                            >  1:1719863/1‑95 (MQ=255)

                                                                                                  tGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGaa                                                            <  2:1719863/95‑1 (MQ=255)

                                                                                                  tGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCa                                                     <  1:322734/102‑1 (MQ=255)

                                                                                                  tGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCa                                                     >  2:322734/1‑102 (MQ=255)

                                                                                                  tGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAGTTGCTGACACGTTTGCAGaaaa                >  1:1103875/1‑139 (MQ=255)

                                                                                                  tGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAGTTGCTGACACGTTTGCAGaaaa                >  2:1184953/1‑139 (MQ=255)

                                                                                                  tGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAGTTGCTGACACGTTTGCAGaaaa                >  1:1167065/1‑139 (MQ=255)

                                                                                                  tGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAGTTGCTGACACGTTTGCAGaaa                 >  1:364253/1‑138 (MQ=255)

                                                                                                  tGTCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAGTTGCTGACACGTTTGCAGaaa                 <  2:364253/138‑1 (MQ=255)

                                                                                                    tCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAGTTGCTGACACGTTTGCAGAAAAg               >  2:901462/1‑138 (MQ=255)

                                                                                                    tCGTGTGCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAGTTGCTGACACGTTTGCAGAAAAg               <  1:901462/138‑1 (MQ=255)

                                                                                                     cGTGTGCTGGGTTCGTTCTATTACCGCCATCCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAGTTGCTGACACGTTTGCAGAAAAGCt             <  1:1160704/139‑1 (MQ=255)

                                                                                                       tgtgCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGc                                                       >  2:573553/1‑95 (MQ=255)

                                                                                                       tgtgCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGc                                                       <  1:573553/95‑1 (MQ=255)

                                                                                                       tgtgCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCa                                                     <  1:209749/97‑1 (MQ=255)

                                                                                                       tgtgCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCa                                                     >  2:209749/1‑97 (MQ=255)

                                                                                                       tgtgCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAGTTGCTGACACGTTTGCAGa                   >  2:1278914/1‑131 (MQ=255)

                                                                                                       tgtgCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAGTTGCTGACACGTTTGCAGa                   <  1:1278914/131‑1 (MQ=255)

                                                                                                       tgtgCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAGTTGCTGACACGTTTGCAGAAAAg               <  2:1579346/135‑1 (MQ=255)

                                                                                                       tgtgCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAGTTGCTGACACGTTTGCAGAAAAg               >  1:1579346/1‑135 (MQ=255)

                                                                                                         tgCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGttt                                                                                            <  1:1505277/56‑1 (MQ=255)

                                                                                                         tgCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGttt                                                                                            >  2:1505277/1‑56 (MQ=255)

                                                                                                         tgCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAg                                                                             <  2:1224166/71‑1 (MQ=255)

                                                                                                         tgCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAg                                                                             >  1:1224166/1‑71 (MQ=255)

                                                                                                         tgCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAGTTGCTGACACGTTTGCAGAAAAGCTGTGa         >  1:840131/1‑139 (MQ=255)

                                                                                                         tgCTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAGTTGCTGACACGTTTGCAGAAAAGCTGTGa         >  1:578506/1‑139 (MQ=255)

                                                                                                           cTGGGTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAGTTGCTGACACGTTTGCAGAAAAGCTGTGata       <  2:296348/139‑1 (MQ=255)

                                                                                                              ggTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGc                                                                                                    >  2:1033824/1‑43 (MQ=255)

                                                                                                              ggTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGc                                                                                                    <  1:1033824/43‑1 (MQ=255)

                                                                                                              ggTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAg                                      <  1:1301653/105‑1 (MQ=255)

                                                                                                              ggTTCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAg                                      >  2:1301653/1‑105 (MQ=255)

                                                                                                              ggTTCGTGCTATTACCGCCAACCAGAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAGTTGCTGACACGTTTGCAGAAAAGCTGTGATATGa    >  2:1096723/1‑139 (MQ=255)

                                                                                                                ttCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAGTTGCTGACACGTTTGCAGAAAAGCTGTGATATGACg  >  2:1645748/1‑139 (MQ=255)

                                                                                                                ttCGTTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAGTTGCTGACACGTTTGCAGAAAAGCTGTGATATGACg  <  1:1184953/139‑1 (MQ=255)

AACTTCCTTGAATCTCGCGGTATGGCACCGATTGCGGAATTTGCAGACCTTTAATTACTAGTAATGGAAATATATTAATGAACGAGTTTTCTATCCTCTGTCGTGTGCTGGGTTCGCTCTATTACCGCCAACCACAAGATCCTTTACTGGTGCCGCTGTTTACCCTGATTCGTGAGGGGAAACTGGCTGCGAACTGGCCACTGGAGCAGGATGAGTTGCTGACACGTTTGCAGAAAAGCTGTGATATGACG  >  NC_000913/1099563‑1099813

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A