BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,490,454	C→T	6.6%	pseudogene (155/258 nt)	yjgX ←	pseudogene fragment

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,490,454	0	C	T	6.6%	2413.4 / 113.2	744	pseudogene (155/258 nt)	yjgX	pseudogene fragment
Reads supporting (aligned to +/- strand): ref base C (307/386); new base T (23/26); total (332/412)
Fisher's exact test for biased strand distribution p-value = 7.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

Only 100 of 756 total aligned reads displayed.

CAGTTGTTCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACGGTGGTCGC  >  CP009273/4490387‑4490520

  gttgttCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGc                                                                  >  1:32130841/1‑68 (MQ=255)

  gttgttCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGc                                                                  >  1:13825629/1‑68 (MQ=255)

    tgttCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCaa                                                                >  1:21533875/1‑68 (MQ=255)

       tCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATg                                                              >  1:22005972/1‑67 (MQ=255)

         aTAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGcc                                                           >  1:3542124/1‑68 (MQ=255)

         aTAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGcc                                                           >  1:26849640/1‑68 (MQ=255)

         aTAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGcc                                                           >  1:33307183/1‑68 (MQ=255)

            aCGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCTGCAATGGCCAAc                                                        >  1:19777347/1‑68 (MQ=255)

            aCGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAAc                                                        <  1:33875871/68‑1 (MQ=255)

            aCGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAAc                                                        <  1:11375785/68‑1 (MQ=255)

            aCGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAAc                                                        <  1:5151562/68‑1 (MQ=255)

            aCGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAAc                                                        >  1:25489130/1‑68 (MQ=255)

            aCGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAAc                                                        <  1:28192984/68‑1 (MQ=255)

              gCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCTGCAATGGCCAACgg                                                      <  1:4144198/68‑1 (MQ=255)

              gCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACgg                                                      <  1:24374853/68‑1 (MQ=255)

              gCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACgg                                                      <  1:18647389/68‑1 (MQ=255)

              gCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACgg                                                      <  1:24709403/68‑1 (MQ=255)

              gCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACgg                                                      <  1:20045027/68‑1 (MQ=255)

              gCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACgg                                                      >  1:10444951/1‑68 (MQ=255)

              gCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACgg                                                      <  1:8386957/68‑1 (MQ=255)

              gCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGACCAACgg                                                      <  1:4883241/68‑1 (MQ=255)

               cTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGt                                                     >  1:26946958/1‑68 (MQ=255)

                tGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGt                                                     <  1:27353805/67‑1 (MQ=255)

                   aTTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTAc                                                 <  1:2793301/68‑1 (MQ=255)

                   aTTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTAc                                                 <  1:686385/68‑1 (MQ=255)

                      tCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACaga                                              <  1:29858756/68‑1 (MQ=255)

                        aCGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCTGCAATGGCCAACGGTTTACAGAGc                                            <  1:1289977/68‑1 (MQ=255)

                        aCGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCTGCAATGGCCAACGGTTTACAGAGc                                            <  1:11743596/68‑1 (MQ=255)

                        aCGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACgg                                                      <  1:9540651/58‑1 (MQ=255)

                        aCGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGc                                            <  1:3046558/68‑1 (MQ=255)

                        aCGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGc                                            <  1:19477652/68‑1 (MQ=255)

                        aCGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGc                                            <  1:7973413/68‑1 (MQ=255)

                        aCGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGc                                            <  1:3091528/68‑1 (MQ=255)

                        aCGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGc                                            <  1:31834709/68‑1 (MQ=255)

                        aCGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGc                                            <  1:15907454/68‑1 (MQ=255)

                        aCGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGc                                            <  1:7534277/68‑1 (MQ=255)

                        aCGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGc                                            <  1:32795438/68‑1 (MQ=255)

                        aCGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGc                                            <  1:16661554/68‑1 (MQ=255)

                         cGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCa                                           <  1:14481816/68‑1 (MQ=255)

                         cGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCa                                           <  1:23667711/68‑1 (MQ=255)

                          gTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCat                                          >  1:30192441/1‑68 (MQ=255)

                          gTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCat                                          >  1:26319454/1‑68 (MQ=255)

                            aaTGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCataa                                        <  1:13492260/68‑1 (MQ=255)

                            aaTGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCata                                         <  1:29069469/67‑1 (MQ=255)

                            aaTGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCata                                         <  1:14890091/67‑1 (MQ=255)

                             aTGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCataat                                       >  1:2509830/1‑68 (MQ=255)

                             aTGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCataat                                       >  1:32501147/1‑68 (MQ=255)

                              tgtgTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCataat                                       >  1:20592521/1‑67 (MQ=255)

                                  tCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGaa                                  >  1:6271743/1‑68 (MQ=255)

                                  tCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGaa                                  >  1:20853068/1‑68 (MQ=255)

                                    aGTTTTCCCCACAACTGTTTCTTTAACCATCCGCAATCGCCAACGGTTTACAGATCATAATACTAATa                                >  1:1567519/1‑68 (MQ=255)

                                      ttGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAg                               >  1:29542222/1‑67 (MQ=255)

                                       tGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATa                                <  1:24001917/65‑1 (MQ=255)

                                       tGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGcc                             <  1:11159973/68‑1 (MQ=255)

                                       tGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGcc                             <  1:28868789/68‑1 (MQ=255)

                                       tGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGcc                             <  1:5435428/68‑1 (MQ=255)

                                       tGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGc                              <  1:12165759/67‑1 (MQ=255)

                                       tGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGc                              <  1:4734364/67‑1 (MQ=255)

                                           cccACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGc                              <  1:9216261/63‑1 (MQ=255)

                                            ccACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACATAGCTTAATACGAATAGCCGTaga                        <  1:17279270/68‑1 (MQ=255)

                                               caACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGagcc                     >  1:17842398/1‑68 (MQ=255)

                                               caACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGagcc                     >  1:23461259/1‑68 (MQ=255)

                                                 aCTGTTCCTTTAACCATCTGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGagcca                    >  1:26059093/1‑67 (MQ=255)

                                                 aCTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGagccag                   <  1:12444156/68‑1 (MQ=255)

                                                 aCTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGagccag                   <  1:589578/68‑1 (MQ=255)

                                                 aCTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGagcca                    >  1:10004241/1‑67 (MQ=255)

                                                 aCTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGagcca                    >  1:28431334/1‑67 (MQ=255)

                                                 aCTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGagcca                    >  1:14672694/1‑67 (MQ=255)

                                                 aCTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGagcca                    >  1:22630229/1‑67 (MQ=255)

                                                 aCTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGagcca                    >  1:22453736/1‑67 (MQ=255)

                                                 aCTGTTCCTTTAACAATATGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGagcca                    >  1:16290223/1‑67 (MQ=255)

                                                    gTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAgccagcca                <  1:3077463/68‑1 (MQ=255)

                                                    gTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAgccagcca                <  1:292812/68‑1 (MQ=255)

                                                    gTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAgccagcca                <  1:19031215/68‑1 (MQ=255)

                                                    gTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAgccagcca                <  1:8640843/68‑1 (MQ=255)

                                                    gTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAgccagcca                <  1:32983971/68‑1 (MQ=255)

                                                    gTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAgccagcca                <  1:13223593/68‑1 (MQ=255)

                                                      tCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGccagccag               <  1:21111579/67‑1 (MQ=255)

                                                      tCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGt              <  1:10168070/68‑1 (MQ=255)

                                                      tCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGt              >  1:2171115/1‑68 (MQ=255)

                                                      tCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGt              >  1:26502437/1‑68 (MQ=255)

                                                      tCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGt              <  1:8984047/68‑1 (MQ=255)

                                                       ccTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGtt             <  1:18181546/68‑1 (MQ=255)

                                                        cTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGtt             >  1:2295682/1‑67 (MQ=255)

                                                           tAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACgg         >  1:18793581/1‑68 (MQ=255)

                                                           tAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACgg         >  1:4593104/1‑68 (MQ=255)

                                                             aCCATCTGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACggtg       >  1:3808223/1‑68 (MQ=255)

                                                             aCCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACggtg       >  1:11552548/1‑68 (MQ=255)

                                                             aCCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACggtg       >  1:14074017/1‑68 (MQ=255)

                                                             aCCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACggtg       >  1:15214880/1‑68 (MQ=255)

                                                             aCCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACggag       >  1:31510129/1‑66 (MQ=255)

                                                             aCCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACg          >  1:25768367/1‑65 (MQ=255)

                                                              ccATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACggtgg      >  1:6570372/1‑68 (MQ=255)

                                                              ccATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACggtgg      >  1:10864928/1‑68 (MQ=255)

                                                              ccATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACggtgg      >  1:7226292/1‑68 (MQ=255)

                                                              ccATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACggtgg      >  1:24889204/1‑68 (MQ=255)

                                                              ccATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACggtgg      <  1:34115451/68‑1 (MQ=255)

                                                              ccATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACggtgg      >  1:3119264/1‑68 (MQ=255)

                                                               cATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGCGCCAGACAGTTACggtgg      >  1:1713080/1‑67 (MQ=255)

                                                                aTCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACGGTGGTc    <  1:17545767/68‑1 (MQ=255)

CAGTTGTTCATAACGCTGCATTTCACGTAATGTGTCAGTTGTCCCCACAACTGTTCCTTTAACCATCCGCAATGGCCAACGGTTTACAGAGCATAATACGAATAGCCGTAGAGCCAGCCAGTTACGGTGGTCGC  >  CP009273/4490387‑4490520

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