BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	1,282,812	C→A	5.8%	intergenic (‑28/+182)	tyrV ← / ← tyrT	tRNA‑Tyr/tRNA‑Tyr

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	1,282,812	0	C	A	5.8%	1214.8 / 3.9	397	intergenic (‑28/+182)	tyrV/tyrT	tRNA‑Tyr/tRNA‑Tyr
Reads supporting (aligned to +/- strand): ref base C (180/182); new base A (6/23); total (192/205)
Fisher's exact test for biased strand distribution p-value = 3.17e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 425 total aligned reads displayed.

TTTACAGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGTTGCCTGTG  >  CP009273/1282746‑1282878

tttACAGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGc                                                                    <  1:19516245/67‑1 (MQ=255)

tttACAGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGc                                                                    <  1:17108347/67‑1 (MQ=255)

tttACAGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGc                                                                    <  1:1747717/67‑1 (MQ=255)

tttACAGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGc                                                                    <  1:25429650/67‑1 (MQ=255)

tttACAGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGc                                                                    <  1:25986911/67‑1 (MQ=255)

tttACAGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCt                                                                   >  1:23280666/1‑68 (MQ=255)

tttACAGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCt                                                                   <  1:28822921/68‑1 (MQ=255)

tttACAGACTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGc                                                                    <  1:15232361/67‑1 (MQ=255)

     aGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGGTTgaga                                                              >  1:36911166/1‑68 (MQ=255)

     aGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTgaga                                                              >  1:25167373/1‑68 (MQ=255)

     aGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTgaga                                                              >  1:12939765/1‑68 (MQ=255)

     aGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTgaga                                                              >  1:14148491/1‑68 (MQ=255)

     aGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTgaga                                                              >  1:36800833/1‑68 (MQ=255)

     aGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTgaga                                                              >  1:39618888/1‑68 (MQ=255)

       tCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCATATTTTGAGGTATTGGGTGAGAtg                                                            >  1:21408868/1‑68 (MQ=21)

       tCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtg                                                            >  1:29540992/1‑68 (MQ=255)

       tCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtg                                                            >  1:10806580/1‑68 (MQ=255)

       tCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtg                                                            >  1:23624700/1‑68 (MQ=255)

       tCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtg                                                            >  1:16629450/1‑68 (MQ=255)

        cTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTgag                                                               <  1:20993543/64‑1 (MQ=255)

        cTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTgag                                                               <  1:10190090/64‑1 (MQ=255)

        cTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTgag                                                               <  1:4646048/64‑1 (MQ=255)

        cTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTgag                                                               <  1:8340358/64‑1 (MQ=255)

        cTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTgag                                                               <  1:12525101/64‑1 (MQ=255)

         ttcTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTATTTCAAATTTTGAGGTAATGCTTGAGAtggt                                                          <  1:18222928/66‑1 (MQ=255)

         tgctgcCTTTGGCCGCTCGGGAAGCCGACCAGTGGTAATTGAAATTTTGTGGTAATGCTTGAGAtggt                                                          <  1:32408126/68‑1 (MQ=25)

         tGCTCCGTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTAAGGTAATGCTTGAGAtggt                                                          <  1:37861143/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGTAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggt                                                          <  1:696760/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggt                                                          <  1:18738208/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggt                                                          <  1:10952409/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggt                                                          <  1:37622342/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggt                                                          <  1:11131949/68‑1 (MQ=255)

            tCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggtggt                                                       >  1:35871118/1‑68 (MQ=255)

            tCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggtgg                                                        <  1:30513488/67‑1 (MQ=255)

            tCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggtgg                                                        <  1:33621703/67‑1 (MQ=255)

             cccTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggtggtg                                                      >  1:50012/1‑68 (MQ=255)

             cccTTTGGCCGCTCGGGAACCCCACCAGGGGGAAATCAATTTTTGAGGTAATGAGTGTTAtggtggtg                                                      >  1:28143660/1‑68 (MQ=18)

               cattGGCCGATCGTGAACCCCACCAGGGGTATTTCATATTTTGAGGTAATGCATGAGATGGTGGTggg                                                    <  1:12709368/66‑1 (MQ=255)

                tttGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTgggg                                                   <  1:34627176/68‑1 (MQ=255)

                tttGGCCGATCGGTAACCCCACCAGGGGTAATTCAAATTTTGATGTAATGCTTGAGATGGTGGTgggg                                                   <  1:6434647/68‑1 (MQ=255)

                   ggCCGCGCGGCAACCCCACGAGGTGTAACTGTAATTTTGAGGTAAAGCTAGAGATGGTGGTGGGGGaa                                                <  1:30006025/68‑1 (MQ=255)

                    gCCGCTCGGGAACCCCACCAGGGGTTATTGATATTTTGAGGGATGGCTTGAGATGGTGGTGGGGGaat                                               >  1:19890558/1‑67 (MQ=25)

                    gCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAg                                               >  1:31822888/1‑68 (MQ=255)

                    gCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAg                                               >  1:13679598/1‑68 (MQ=255)

                    gCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAg                                               >  1:8873837/1‑68 (MQ=255)

                    gCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAg                                               >  1:36416240/1‑68 (MQ=255)

                    gCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAg                                               >  1:10013826/1‑68 (MQ=255)

                    gCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAg                                               >  1:28610361/1‑68 (MQ=255)

                    gCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTCAGGAAATCGCGGTTATGGGGGTGGGGGAAg                                               >  1:31519173/1‑68 (MQ=16)

                     ccGCTCGGGAACCCCACCAGGGGTAAATCAAATTTAGAGGTAATGAGTGAGATGGTGGTGGGGGAAgg                                              >  1:11605773/1‑68 (MQ=38)

                     ccGCTCGGCAACGCCCCGAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAgg                                              <  1:34316952/68‑1 (MQ=255)

                      cGCTCGGTAACCCCACCATGGGTAATTCAAATTTTGAGGTAATGCTAGAGATGGTGGTGGGGGAAgg                                              <  1:31061805/67‑1 (MQ=255)

                      cGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGCGGTAATGCTTGAGATGGTGGTGGGGGAAgg                                              <  1:9765706/67‑1 (MQ=255)

                      cGCACGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAgg                                              <  1:21791317/67‑1 (MQ=255)

                          cGGTAACCCCACCAGGGGTAATTCAAATTTTGAGGTTATGCTTGAGATGGTGGTGGGGGAAGGattat                                         <  1:17383341/68‑1 (MQ=255)

                               aCCCCACCAGGGGTAATTCATATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATtcgtc                                    >  1:21210055/1‑68 (MQ=255)

                                 cccACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATtcgtc                                    >  1:10352536/1‑66 (MQ=255)

                                  ccaccaGGGGTAATTAAATTTTTGCGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGtcgct                                 <  1:17555820/68‑1 (MQ=38)

                                   caccaGGGGTAATTCAATTTTTGAGGTAATGCGTGAGATGGTGGTGGGGGAAGGATTATTCGtcgct                                 >  1:21741973/1‑67 (MQ=255)

                                    accaGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttc                               >  1:28542203/1‑68 (MQ=255)

                                     ccaGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttc                               >  1:5246409/1‑67 (MQ=255)

                                      caGGTGTAATTCAATTTTTGTGTTTAAGCAAGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgc                             <  1:6324100/68‑1 (MQ=18)

                                       atgggTATTTCAAATTTTGATGTAATGCATGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgct                            <  1:31592615/66‑1 (MQ=37)

                                       aGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgc                             >  1:20181400/1‑67 (MQ=255)

                                       aGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgc                             >  1:9497707/1‑67 (MQ=255)

                                       aGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgc                             >  1:7533049/1‑67 (MQ=255)

                                       aGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgc                             >  1:38997190/1‑67 (MQ=255)

                                       aGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgc                             >  1:19031487/1‑67 (MQ=255)

                                       aGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgc                             >  1:32181979/1‑67 (MQ=255)

                                        ggggTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgct                            >  1:32935698/1‑67 (MQ=255)

                                         gggTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgct                            >  1:15885015/1‑66 (MQ=255)

                                         gggTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgct                            >  1:22880105/1‑66 (MQ=255)

                                          gttAATTAAAATATTGAGGTAATGATAGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcc                          <  1:38317411/65‑1 (MQ=37)

                                          ggTTATTCAATTTTTGATGTATTGATTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcct                         <  1:20432186/68‑1 (MQ=37)

                                          ggTAATTCAAATTTTGCGGTATTGCTTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgct                            <  1:25872679/65‑1 (MQ=255)

                                          ggTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgct                            <  1:1479337/65‑1 (MQ=255)

                                          ggTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcc                          >  1:15088532/1‑67 (MQ=255)

                                          ggTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcc                          >  1:558489/1‑67 (MQ=255)

                                          ggTAATTCAAATTTTGAGGTAATGCTAGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgct                            <  1:7244693/65‑1 (MQ=255)

                                           gTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTAGTCGCTTCGctcctc                        >  1:36162566/1‑68 (MQ=255)

                                            tAATTCAAATTTTGCGCTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcctc                        <  1:9133244/67‑1 (MQ=255)

                                            tAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcctc                        >  1:24123837/1‑67 (MQ=255)

                                            tAATTCAAATTTTGAGGTAATGCATGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcctc                        <  1:4361122/67‑1 (MQ=255)

                                            tAATTCAAATTTTGAGGTAATGATTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcctc                        <  1:15602502/67‑1 (MQ=255)

                                               ttCAAATTTTGATGTAATGATTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCAccc                    <  1:26384742/68‑1 (MQ=255)

                                               ttCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTACGCGCATCAccc                    >  1:35134706/1‑68 (MQ=37)

                                                tCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCt                   >  1:22274523/1‑68 (MQ=255)

                                                    aTTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCgg               >  1:27580274/1‑68 (MQ=255)

                                                    aTTATGAGCTAATGATTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCgg               <  1:2270066/68‑1 (MQ=37)

                                                      tttGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCggg              >  1:29815991/1‑67 (MQ=255)

                                                      tttGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGc             <  1:17679525/68‑1 (MQ=255)

                                                      tttGAGGTAATGATTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGc             <  1:33237219/68‑1 (MQ=255)

                                                       ttGAGGTTATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGcc            <  1:5911744/68‑1 (MQ=255)

                                                         gacgTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGt          <  1:16430647/65‑1 (MQ=255)

                                                         gAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGt          <  1:7888099/68‑1 (MQ=255)

                                                            gTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGTTg        >  1:35734774/1‑67 (MQ=255)

                                                            gTAATGCTCGTGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGTTGc       <  1:26985537/68‑1 (MQ=255)

                                                              aaTGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGTTg        >  1:24421817/1‑65 (MQ=255)

                                                              aaTGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGTTGCCt     <  1:12144931/68‑1 (MQ=255)

                                                                  cTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGTTGCCtgtg  >  1:26696334/1‑67 (MQ=255)

TTTACAGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGTTGCCTGTG  >  CP009273/1282746‑1282878

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