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
A3 F14 I0 R1	206	76.7	3255580	98.8%	3216513	146.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947_CJ‑RC	1,258,397	T→G	24.1%	S203R (AGC→CGC)	PP_1102 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947_CJ‑RC	1,258,397	0	T	G	24.1%	64.0 / 2.9	40	S203R (AGC→CGC)	PP_1102	hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (24/6); new base G (3/7); total (27/13)
Fisher's exact test for biased strand distribution p-value = 6.48e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCGATACCCCGCAACCGCCGGAACCCGGTGAGACGCCTCCCATGGAGCCGGGTGAGCCGACCTTGCCGGACGAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGCTCATCGATCACGAAGCAAGGCAGGCGCAAGCGCTGACGGGCCTTGCCGCGCAGGACGAAGACCGGGTGTACATG  >  NC_002947_CJ‑RC/1258249‑1258538

ccGATACCCCGCAACCGCCGGAACCCGGTGAGACGCCTCCCATGGAGCCGGGTGAGCCGACCTTGCCGGACGAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGgct                                                                                                                                               >  3:82385/1‑149 (MQ=255)

 cGATACCCCGCAACCGCCGGAACCCGGTGAGACGCCTCCCATGGAGCCGGGTGAGCCGACCTTGCCGGACGAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGgct                                                                                                                                               <  8:394419/148‑1 (MQ=255)

       cccGCAACCGCCGGAACCCGGTGAGACGCCTCCCATGGAGCCGGGTGAGCCGACCTTGCCGGACGAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGgctggcgct                                                                                                                                         <  6:290086/148‑1 (MQ=255)

       cccGCAACCGCCGGAACCCGGTGAGACGCCTCCCATCGAGCCGGCTGAGCCGACCTTGCCGGACGAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCCGCCAGACGCGTTCAGCCCCAGCCACGTACATCCCgcaggcccag                                                                                                                                        >  3:35269/1‑145 (MQ=255)

        ccGCAACCGCCGGAACCCGGTGAGACGCCTCCCATGGAGCCGGGTGAGCCGACCTTGCCGGACGAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGgctggcgctgg                                                                                                                                       >  3:167082/1‑149 (MQ=255)

        ccGCAACCGCCGGAACCCGGTGAGACGCCTCCCATGGAGCCGGGTGAGCCGACCTTGCCGGACGAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGgctggcgctg                                                                                                                                        >  8:253527/1‑148 (MQ=255)

         cGCAACCGCCGGAACCCGGTGAGACGCCTCCCATGGAGCCGGGTGAGCCGACCTTGCCGGACGAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACCGCCGgctggcgctgg                                                                                                                                       >  7:289089/1‑148 (MQ=255)

          gCAACCGCCGGAACCCGGTGAGACGCCTCCCATGGAGCCGGGTGAGCCGACCTTGCCGGACGAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGgctggcgctggc                                                                                                                                      >  5:373954/1‑148 (MQ=255)

               cgccgGAACCCGGTGAGACGCCTCCCATGGAGCCGGGTGAGCCGACCTTGCCGGACGAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGGCTGGCGCTGGCTGGGGt                                                                                                                                >  2:333809/1‑149 (MQ=255)

                 ccgGAACCCGGTGAGACGCCTCCCATGGAGCCGGGTGAGCCGACCTTGCCGGACGAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCCCCAGCCAGGTACAGCCGGCTGGCGCTGGCgggggga                                                                                                                               >  5:225443/1‑146 (MQ=255)

                         cGGTGAGACGCCTCCCATGGAGCCGGGTGAGCCGACCTTGCCGGACGAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCCAc                                                                                                                      >  2:308206/1‑149 (MQ=255)

                                     tCCCATGGAGCCGGGTGAGCCGACCTTGCCGGACGAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAAc                                                                                                          >  1:286579/1‑149 (MQ=255)

                                      cccATGGAGCCGGGTGAGCCGACCTTGCCGGACGAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAAc                                                                                                          >  8:203321/1‑148 (MQ=255)

                                        cATGGAGCCGGGTGAGCCGACCTTGCCGGACGAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCCGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACt                                                                                                         >  5:212118/1‑147 (MQ=255)

                                               ccGGGTGTGCGCACTTTGCCGGACGCCCCGCCACCCCCCCGTGTGGCGTGAGGGTCCATAAAGCTCCCATACGCGTTCAGCCCCACCATTGTACCGCCGGGTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGaa                                                                                                  <  6:392234/147‑1 (MQ=255)

                                                ggggTGTGCCGACCTGGCGGGCGGCGCGGCCTCCCGCCCGTGTGGCCTGTGCGGGGTTAACGCGCCCACCGGGTTTCCGCGCCCGCCTGGTACCGCGGGGGGGGGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATg                                                                                                <  6:327660/147‑1 (MQ=255)

                                                 gggTGAGCCGACCTTGCCGGACGAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCAACCCCCCGGTGAACTCACCGAATg                                                                                                >  4:386097/1‑147 (MQ=255)

                                                  ggTGAGCCGACCTTGCGGGACGACCCGCCACCCGCCCCTGGGGCGTGAGCGTCGCTAACGCGGCCAGCCGCTTTCAGCGCCAGCCAGTTACCGCCGGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCa                                                                                              <  8:342454/148‑1 (MQ=255)

                                                   gTGCGCCGACCTTGCGGGACGAGCCGCCCCCCGCCCCTGTGGCCTGAGCGGCGCTAACGCGGCCTGACGCGTTCCGCGCCAGCCAGTTACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAg                                                                                             <  8:141680/148‑1 (MQ=255)

                                                    tGAGCCGACCTTGCCGGACGAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAgg                                                                                            >  5:349833/1‑148 (MQ=255)

                                                      cgCCCACTTTGCCGTACGTGCCGCGCCCGGCCCCTGTGGCTTGAGGGTGGTTAATGGGGCCTGCGGGTTTCTGGGCCACCCTGGTACCGCGGGGGGGGGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGt                                                                                           <  8:114631/146‑1 (MQ=255)

                                                       gCCGACCTTGCCGGACGAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGATCAGCGCCAGCCAGGTACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAAAGCAGGTAg                                                                                         >  2:59265/1‑148 (MQ=255)

                                                        ccGACCTTGCCGCACGCCCCGCCTCCCCCCCCTGGGGCGTGAGGTTCGCTAATGCGGCCAGACGGTTTCCGCGCCCGCCTGGAACCGCCGGGTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGc                                                                                        <  6:349833/148‑1 (MQ=255)

                                                              ttGCCGGACGAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCCGGTACAGCCGGCGGGCGCTGGCGGGGGGGATTTACCCCCCCCCGGTGAACTCACCGAATGGAGGTTGCAGGcgt                                                                                  >  5:10758/1‑146 (MQ=255)

                                                                   ggACGAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGc                                                                            >  1:216631/1‑149 (MQ=255)

                                                                   ggACGAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGGCGGGCGCTGGCGGGGGGGGTTTCCCACCCCCCCGTGAACTCACCGAAAGCAGGTAGCAGGCTGACATg                                                                             >  5:273425/1‑148 (MQ=255)

                                                                       gAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGCtaa                                                                         >  2:188924/1‑146 (MQ=255)

                                                                       gAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGCTCa                                                                         >  2:183474/1‑148 (MQ=255)

                                                                        aGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGGCTGGCGCTGGCCGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGCTCAt                                                                        >  8:301311/1‑148 (MQ=255)

                                                                            gccCCCCGCCCCTGGGGCCTGAGGGTCGCTAACGCGGCCAGACGCGTTCCGCGCCAGCCAGGTACAGCCGGCGGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGCTCATCGATc                                                                   <  2:286579/149‑1 (MQ=255)

                                                                                        tgtgGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGCTCATCGATCACGAAGCAagg                                                        >  2:371633/1‑148 (MQ=255)

                                                                                          tgGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGCTCATCGATCACGAAGCAaggca                                                      <  6:373954/148‑1 (MQ=255)

                                                                                             ccTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCCGGTACAGCCGGCGGGCGCGGGCGGGGGTGTTTTCCCCCCCCCCGGTGAACTCCCCGAATGCAGGTAGCAGGCGGCCTTGCTGATGGCTCACGACGCAAGGCAGgcg                                                  >  3:59640/1‑149 (MQ=255)

                                                                                                gAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGCTCATCGATCACGAAGCAAGGCAGgcgc                                                 >  3:55798/1‑147 (MQ=255)

                                                                                                 aGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGCTCATCGATCACGAAGCAAGGCAGGCGCAAg                                              >  2:90070/1‑149 (MQ=255)

                                                                                                    gTCGCTAACGCGGCATGAGGGTTTCAGCGCCAGCCTGTTACCGCGGGGGGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGCTCATCGATCACGAAGCAAGGCAGGCGCAAgcgc                                           <  4:107288/149‑1 (MQ=255)

                                                                                                     tCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCGGACTTGCTCATCGCTCACGAAGCAAGGCAGGCGCAAgcgc                                           >  7:105469/1‑148 (MQ=255)

                                                                                                         tAACGCGGCCAGACGCGTTCAGCGCCCGCCAGGTACCGCGGGGGGGCGCTGGCGGGGGTGATTTCCCAACCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGCTCATCGATCACGAAGCAAGGCAGGCGCAAGCGCTGAc                                       <  8:41935/148‑1 (MQ=255)

                                                                                                         tAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCCGCTGGCGCTGGCGGGGGTGATTTACCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGCACATCGAACACGAAGCAAGGCAGGCGCAAGCGCTGACg                                      >  1:348202/1‑149 (MQ=255)

                                                                                                               ggCCAGACGGTTTCAGCGCCAGCCTGGTACCGCGGGGGGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGCTCATCGATCACGAAGCAAGGCAGGCGCAGGCGCTGACGGGCCt                                 <  8:223044/148‑1 (MQ=255)

                                                                                                                 ccAGACGCGTTCAGCGCCAGCCAGGTACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGCTCATCGATCACGAAGCAAGGCAGGCGCAAGCGCTGACGGGCCTTGc                              >  3:161341/1‑149 (MQ=255)

                                                                                                                   aGACGCGTTCAGCGCCAGCCAGGTACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGCTCATCGATCACGAAGCAAGGCAGGCGCAAGCGCTGACGGGCCTTGCcg                            >  3:232969/1‑149 (MQ=255)

                                                                                                                       gcgTTCCGCGCCAGCCAGGAACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGCTCATCGATCACGAAGCAAGGCAGGCGCAAGCGCTGACGGGCCTTGCCgcgc                         <  6:172410/148‑1 (MQ=255)

                                                                                                                               cgcCAGCCAGGTACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGCTCATCGATCACGAAGCAAGGCAGGCGCAAGCGCTGACGGGCCTTGCCGCGCAGGACg                   >  6:336287/1‑146 (MQ=255)

                                                                                                                                    gcctgGTCCCGCGGGCGGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGCTCATCGATCACGAAGCAAGGCAGGCGCAAGCGCTGACGGGCCTTGCCGCGCAGGACGAAGACCg            <  6:125344/148‑1 (MQ=255)

                                                                                                                                    gccagGTACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGCTCATCGATCACGAAGCAAGGCAGGCGCAAGCGCTGACGGGCCTTGCCGCGCAGGACGAAGACCgg           >  1:11071/1‑149 (MQ=255)

                                                                                                                                      cagGTACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGCTCATCGATCACGAAGCAAGGCAGGCGCAAGCGCTGACGGGCCTTGCCGCGCAGGACGAAGACCggg          >  8:163385/1‑148 (MQ=255)

                                                                                                                                          tACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGCTCATCGATCACGAAGCAAGGCAGGCGCAAGCGCTGACGGGCCTTGCCGCGCAGGACGAAGACCGGGTGTa      >  2:226389/1‑148 (MQ=255)

                                                                                                                                              gcgggcgggcgCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGCTCATCGATCACGAAGCAAGGCAGGCGCAAGCGCTGACGGGCCTTGCCGCGCAGGACGAAGACCGGGTGTACATg  <  8:289089/145‑1 (MQ=255)

CCGATACCCCGCAACCGCCGGAACCCGGTGAGACGCCTCCCATGGAGCCGGGTGAGCCGACCTTGCCGGACGAGCCGCCTCCCGCCCCTGTGGCCTGAGCGTCGCTAAAGCGGCCAGACGCGTTCAGCGCCAGCCAGGTACAGCCGGCTGGCGCTGGCGGGGGTGATTTCCCACCCCCCGGTGAACTCACCGAATGCAGGTAGCAGGCTGACTTGCTCATCGATCACGAAGCAAGGCAGGCGCAAGCGCTGACGGGCCTTGCCGCGCAGGACGAAGACCGGGTGTACATG  >  NC_002947_CJ‑RC/1258249‑1258538

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