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 I2 R1	92	50.6	2362856	94.3%	2228173	111.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	585,217	C→T	W139* (TGG→TGA)	ompT ←	DLP12 prophage, outer membrane protease VII, outer membrane protein 3b

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	585,217	0	C	T	100.0%	186.1 / NA	54	W139* (TGG→TGA)	ompT	DLP12 prophage, outer membrane protease VII, outer membrane protein 3b
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (29/25); total (29/25)

AAGGAGCCGATATCATCTCTGAATCCCTCCTCAGAACTGTAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGCCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCCAGTCCTGATCGACCATATTGCCACCTCGGCTGCC  >  NC_000913/585086‑585351

aaGGAGCCGATATCATCTCTGAATCCCTCCTCAGAACTGTAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCtt                                                                                                                                 >  2:908960/1‑139 (MQ=255)

    aGCCGATATCATCTCTGAATCCCTCCTCAGAACTGTAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGat                                                                                                                             >  2:610515/1‑139 (MQ=255)

       cGATATCATCTCTGAATCCCTCCTCAGAACTGTAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATAtt                                                                                                                          <  2:368738/139‑1 (MQ=255)

              atcTCTGAATCCCTCCTCAGAACTGTAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCa                                                                                                                   >  2:567670/1‑139 (MQ=255)

                     aaTCCCTCCTCAGAACTGTAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGt                                                                                                            >  2:200487/1‑139 (MQ=255)

                          ctcctcAGAACTGTAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTggta                                                                                                       >  2:785549/1‑137 (MQ=255)

                          ctcctcAGAACTGTAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCa                                                                                                       >  1:246841/1‑139 (MQ=255)

                          ctcctcAGAACTGTAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCa                                                                                                       >  2:1097245/1‑139 (MQ=255)

                          ctcctcAGAACTGTAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCa                                                                                                       >  1:231271/1‑139 (MQ=255)

                                aGAACTGTAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTg                                                                                                 <  1:1131615/139‑1 (MQ=255)

                                aGAACTGTAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTg                                                                                                 <  2:1168314/139‑1 (MQ=255)

                                    cTGTAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGTATAATTGAGtt                                                                                             <  1:785549/139‑1 (MQ=255)

                                    cTGTAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGtt                                                                                             <  1:908960/139‑1 (MQ=255)

                                    cTGTAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGtt                                                                                             <  1:1022426/139‑1 (MQ=255)

                                       tAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGagtcagc                                                                                                                                    >  2:1107257/1‑97 (MQ=255)

                                       tAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGagtcagc                                                                                                                                    <  1:1107257/97‑1 (MQ=255)

                                       tAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTtgtg                                                                                          >  1:822750/1‑139 (MQ=255)

                                       tAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTtgtg                                                                                          >  1:39141/1‑139 (MQ=255)

                                       tAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTtgtg                                                                                          >  1:41847/1‑139 (MQ=255)

                                       tAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTCTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTCGGCATAATTGAGTtgtg                                                                                          >  2:724695/1‑139 (MQ=255)

                                          atatAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTAt                                                                                       <  1:1178210/139‑1 (MQ=255)

                                           tataGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATc                                                                                      <  2:39141/139‑1 (MQ=255)

                                               ggAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAggg                                                                                  <  1:1178165/139‑1 (MQ=255)

                                                 aaCCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTgg                                                                                                         <  1:1115102/114‑1 (MQ=255)

                                                 aaCCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTgg                                                                                                         >  2:1115102/1‑114 (MQ=255)

                                                 aaCCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGgtg                                                                                >  1:424190/1‑139 (MQ=255)

                                                 aaCCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGgtg                                                                                >  2:878899/1‑139 (MQ=255)

                                                   ccaccTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATAtt                                                                                                                          >  1:271555/1‑95 (MQ=255)

                                                   ccaccTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATAtt                                                                                                                          <  2:271555/95‑1 (MQ=255)

                                                     accTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCa                                                                                                       <  1:797588/112‑1 (MQ=255)

                                                     accTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCa                                                                                                       >  2:797588/1‑112 (MQ=255)

                                                      ccTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGagtcagc                                                                                                                                    >  1:93883/1‑82 (MQ=255)

                                                      ccTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGagtcagc                                                                                                                                    <  2:93883/82‑1 (MQ=255)

                                                       ctctGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCaaa                                                                                                                 <  2:781482/100‑1 (MQ=255)

                                                       ctctGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCaaa                                                                                                                 >  1:781482/1‑100 (MQ=255)

                                                          tGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGt                                                                                                            <  1:960959/102‑1 (MQ=255)

                                                          tGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGt                                                                                                            >  2:960959/1‑102 (MQ=255)

                                                                tAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGt                                                                 <  2:890806/139‑1 (MQ=255)

                                                                    gCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAg                                                             <  1:878899/139‑1 (MQ=255)

                                                                      tataACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGt                                                           >  2:552021/1‑139 (MQ=255)

                                                                        taACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTc                                                         >  2:913716/1‑139 (MQ=255)

                                                                               tttCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGtt                                                  >  2:95763/1‑139 (MQ=255)

                                                                                ttCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTa                                                 >  1:577623/1‑139 (MQ=255)

                                                                                 tCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTAc                                                <  2:96928/139‑1 (MQ=255)

                                                                                           cGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCTGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTAAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAatccat                                      <  1:102700/139‑1 (MQ=255)

                                                                                           cGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAatccat                                      >  2:289809/1‑139 (MQ=255)

                                                                                             gCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTg                                                                                                 <  2:779147/78‑1 (MQ=255)

                                                                                             gCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTg                                                                                                 >  1:779147/1‑78 (MQ=255)

                                                                                             gCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAg                                                                                               <  2:386023/80‑1 (MQ=255)

                                                                                             gCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAg                                                                                               >  1:386023/1‑80 (MQ=255)

                                                                                                    gTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGtt                                                                                             >  2:252763/1‑75 (MQ=255)

                                                                                                    gTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGtt                                                                                             <  1:252763/75‑1 (MQ=255)

                                                                                                        cAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCCAGTCCTGATCg                         <  2:231271/139‑1 (MQ=255)

                                                                                                               tAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATc                                                                                      <  2:472185/71‑1 (MQ=255)

                                                                                                               tAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATc                                                                                      >  1:472185/1‑71 (MQ=255)

                                                                                                                         cGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGATTTGTGTATCAGGGTGTCTACTTTCa                                                                      >  1:725296/1‑77 (MQ=255)

                                                                                                                         cGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTct                                                                      <  2:725296/77‑2 (MQ=255)

                                                                                                                               ggagTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCCAGTCCTGATCGACCATATTGCCACCTCGGCTGcc  <  2:822750/139‑1 (MQ=255)

AAGGAGCCGATATCATCTCTGAATCCCTCCTCAGAACTGTAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGCCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCCAGTCCTGATCGACCATATTGCCACCTCGGCTGCC  >  NC_000913/585086‑585351

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A