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
A2 F13 I0 R1	203	85.6	3649704	98.8%	3605907	146.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947_CJ‑RC	3,447,286	A→C	27.0%	S18R (AGC→CGC)	PP_5556 →	bacteriophage lysis protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947_CJ‑RC	3,447,286	0	A	C	27.0%	50.4 / 7.3	51	S18R (AGC→CGC)	PP_5556	bacteriophage lysis protein
Reads supporting (aligned to +/- strand): ref base A (23/9); new base C (11/3); total (34/17)
Fisher's exact test for biased strand distribution p-value = 7.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGGGCGACATCCTGGCGATCACCAAACGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTGCAGCAGCAGC  >  NC_002947_CJ‑RC/3447138‑3447431

aGGGCGACATCCTGGCGATCACCAAACGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCa                                                                                                                                                   <  3:56860/149‑1 (MQ=255)

 gggCGACATCCTGGCGATCACCAAACGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAg                                                                                                                                                  >  7:404262/1‑149 (MQ=255)

  ggCGACATCCTGGCGATCACCAAACGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAgc                                                                                                                                                 <  8:245237/149‑1 (MQ=255)

     gACATCCTGGCGATCACCAAACGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCt                                                                                                                                              >  5:65055/1‑149 (MQ=255)

       cATCCTGGCGATCACCAAACGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTgg                                                                                                                                            <  1:282414/149‑1 (MQ=255)

           cTGGCGATCACCAAACGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTggcggc                                                                                                                                        >  5:412111/1‑149 (MQ=255)

            tGGCGATCACCAAACGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCACCGCTGgcggcg                                                                                                                                       >  3:288580/1‑149 (MQ=255)

              gCGATCACCAAACGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGcc                                                                                                                                     >  8:299564/1‑149 (MQ=255)

                     ccAAACGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCCCGCTGGCGGCGCCCGGGCAg                                                                                                                              >  3:344473/1‑149 (MQ=255)

                     ccAAACGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCCCGCGCGCGGCGCCCGGGCAg                                                                                                                              >  3:54248/1‑149 (MQ=255)

                     ccAAACGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGTGGCGCCCGGGCAg                                                                                                                              >  2:432470/1‑149 (MQ=255)

                     ccAAACGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGTGGCGCCCGGGCAg                                                                                                                              >  2:438568/1‑149 (MQ=255)

                       aaaCGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCCCTGGCGGCGCCCGGgccgcc                                                                                                                            >  5:363828/1‑149 (MQ=255)

                          cttATCATTTGTGGTAGCACGGGTGTGGAGTAGCGCTAGGCCCTATACACGCGCGCGCGCTTGGTGCTGCTGTGAGGGGTGGGGCCACCCGCCTGGGCGCGGTGGCGGTGGTGGTGGCCGCCTGCGCGGGCGGCGCCCGGGCAGCCTgg                                                                                                                         <  6:180137/147‑1 (MQ=255)

                              tCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCGGGCGGCGCCCGGGCAGCCTGGgtgt                                                                                                                     >  8:193543/1‑149 (MQ=255)

                                       gtAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCAGGCGGCGCCCCGGCAGCCAGGGTGTGGCAGGcc                                                                                                             >  2:416706/1‑148 (MQ=255)

                                        tAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGccca                                                                                                           >  7:297856/1‑147 (MQ=255)

                                        tAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCCCCACCGCTCGCCGCCCCCGGGCAGCCAGGGTGTGGCAGGCCaa                                                                                                           >  6:199264/1‑149 (MQ=255)

                                          gCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACg                                                                                                         >  8:140377/1‑149 (MQ=255)

                                             aCGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCAGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGcc                                                                                                       >  1:284883/1‑148 (MQ=255)

                                              cGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCCCTGGCGGCGCCCCGGCAGCCAGGGTGTGGCAGGCCAACCCCta                                                                                                     >  4:178760/1‑149 (MQ=255)

                                                    ggaggaTCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAAc                                                                                                          >  7:329018/1‑138 (MQ=255)

                                                      aggaTCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCGGGGGGTGGCAGGCCCACGCCGATAAGgcgc                                                                                             >  3:410693/1‑149 (MQ=255)

                                                             cAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTGGCGGCGCCCGGGCAGCCGGGGTGTGGCAGGCCAACGCCGATAAGGCGCAGCTCGc                                                                                      >  5:60062/1‑149 (MQ=255)

                                                                 ccccTATACTCGCGCGCGCTCGTGGTGCTGCTGTGCGGGGTTGGGCCCCCCGCGTGGGCGCGGTGGCGGTGGTGCGGGCCCCCTGGGGGGGGGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGAt                                                                                  <  2:358482/148‑1 (MQ=255)

                                                                    ctctACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACCCCGATAAGGCGCAGCTCGCGGATAAg                                                                               >  8:169209/1‑149 (MQ=255)

                                                                     tctACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCCCGCAGGCGGCGCCCCGGCCGCCGGGGGGTGGCAGGCCAACCCCGATAAAGCGCACCTCGCGGATCAgg                                                                              >  2:182939/1‑149 (MQ=255)

                                                                     tctACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAgg                                                                              >  8:308849/1‑149 (MQ=255)

                                                                       tACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGTGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGcc                                                                            <  1:438568/149‑1 (MQ=255)

                                                                       tACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGGGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGcc                                                                            <  1:432470/149‑1 (MQ=255)

                                                                          aaGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGAt                                                                         >  8:14529/1‑149 (MQ=255)

                                                                           agcgagcgCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGAt                                                                         >  7:366731/1‑148 (MQ=255)

                                                                                gcgcTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTGGCGGCGCCCCGGCAGCCGGGGTGTGGGAGGCCAACGCCTATAAGGGGCCGCTCGCGGATAAGGCCGAGGACt                                                                     >  4:323834/1‑147 (MQ=255)

                                                                                gcgcTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCCCCACCCCTGGCGGCGCCCCGGCACCCGGGGTGTGGCAGGCCAACGCCGATAATGAGCAGCTCGCTGATAAGGCCGATTACTTc                                                                   >  2:365507/1‑149 (MQ=255)

                                                                                   cTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCgg                                                                 >  7:155422/1‑148 (MQ=255)

                                                                                               gaGTGTGCGTTTGGGCCCCGCGGGTGGTGGCGGGGGCGGTGCTGCTGGCCGCCTGGGTTGGGGGCGCCCGTGCAGCCTGTGTGTGGCAGGCGAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGc                                                     <  6:115717/147‑1 (MQ=255)

                                                                                                    cgggcTGGGGCCCCCCGCCTGGGCGCGGGGGCGCTGCTGCGGGCCGCCCGCGGGGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGaa                                               <  7:107903/146‑1 (MQ=255)

                                                                                                    cgcgcTGGGGCCCCCCGCCTGGGCGCGGGGGCGCTGCGGCGGGCCGCCCGGGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGgaga                                                <  5:362150/147‑1 (MQ=255)

                                                                                                      ggcgggcgCCCCCCGGGTGGCCGCCGGGGCGCGGCTGCTGGCCGGCAGCGCGGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAgg                                             <  5:114787/142‑1 (MQ=255)

                                                                                                            ggCCACCCGCCTGGGCGCCGTGGCGCTGGTGCTGGCCGCCTGCGCGGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATcgc                                        <  1:306634/148‑1 (MQ=255)

                                                                                                               cACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCgcgcgc                                    >  7:283045/1‑149 (MQ=255)

                                                                                                                 cccGCCTGGGCGGGGGGGCGCGGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCAc                                  <  2:235947/149‑1 (MQ=255)

                                                                                                                  ccGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCGATAAGGCGCAGCTCGCTGATAAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACg                                 >  8:163514/1‑149 (MQ=255)

                                                                                                                       tGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTg                            <  7:299564/149‑1 (MQ=255)

                                                                                                                        ggTCGCCGTGGCGCTGCTGCTGGCCGCCCCCGCTGGCGGCGCCCCGGCAGCCTGGGTGTGGCAGGCCAACCCCAATAATGCGCAGCTCGCGGATAAGGCCGATGACTTAGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACCGTCTgg                           >  4:317426/1‑149 (MQ=255)

                                                                                                                             ccGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCgg                      <  8:297856/149‑1 (MQ=255)

                                                                                                                                gggCGGTGCTGCTGGCCGCCCGCGGTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGgag                   <  6:162593/148‑1 (MQ=255)

                                                                                                                                   cgcTGCTGCTGCGCTCCAGCGCGGGGGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAg                <  7:318547/149‑1 (MQ=255)

                                                                                                                                          gctgGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTgcag         >  4:170998/1‑149 (MQ=255)

                                                                                                                                            gggCCGCCTGGGGGGGGGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTgcagca       <  4:410693/148‑1 (MQ=255)

                                                                                                                                                 gccAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGATGGCTGCagcagcagc  >  6:158513/1‑149 (MQ=255)

                                                                                                                                                 gccAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGACGGCTGCagcagcagc  >  4:368888/1‑149 (MQ=255)

AGGGCGACATCCTGGCGATCACCAAACGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTGCAGCAGCAGC  >  NC_002947_CJ‑RC/3447138‑3447431

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A