BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,382,371	G→T	7.2%	intergenic (+7/‑29)	glyX → / → glyY	tRNA‑Gly/tRNA‑Gly

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,382,371	0	G	T	7.2%	984.5 / 6.2	355	intergenic (+7/‑29)	glyX/glyY	tRNA‑Gly/tRNA‑Gly
Reads supporting (aligned to +/- strand): ref base G (93/220); new base T (15/16); total (108/247)
Fisher's exact test for biased strand distribution p-value = 4.19e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 355 total aligned reads displayed.

TAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGC  >  CP009273/4382308‑4382434

tAGAGCACGACCTTGCCAAGGTCTGGGTCTAGAGTTCTAGTCTCGTTTCCCGCGCCAAAATTTGAAAg                                                             >  1:5572404/1‑68 (MQ=11)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAg                                                             >  1:3095851/1‑68 (MQ=31)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAg                                                             >  1:4972146/1‑68 (MQ=31)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAg                                                             >  1:4619398/1‑68 (MQ=31)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGt                                                            >  1:3787215/1‑68 (MQ=18)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                            <  1:33435621/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                            <  1:1956855/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                            <  1:35683316/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                            <  1:35881317/68‑1 (MQ=33)

  gagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGATAGt                                                            >  1:37561094/1‑67 (MQ=14)

  gagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                            >  1:245224/1‑67 (MQ=33)

    gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                            >  1:11326822/1‑65 (MQ=33)

    gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGc                                                          <  1:27887967/67‑1 (MQ=37)

    gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGc                                                          <  1:36200956/67‑1 (MQ=37)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCt                                                         <  1:38920721/66‑1 (MQ=39)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCt                                                         <  1:36532214/66‑1 (MQ=39)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCt                                                         <  1:33269199/66‑1 (MQ=39)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCt                                                         <  1:10318955/66‑1 (MQ=39)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                       <  1:21647582/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                       <  1:31426452/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                       <  1:38380852/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                       <  1:36898919/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                       >  1:16911008/1‑68 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                       <  1:15910305/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                       <  1:15292510/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                       <  1:6337659/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                       <  1:6775204/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                       <  1:13034595/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGATGt                                                       >  1:22887798/1‑68 (MQ=255)

      aCGACCTTGCCAAGGGCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                       <  1:32530592/68‑1 (MQ=255)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTATAGTGATGTAAg                                                    >  1:35271270/1‑68 (MQ=14)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTTATAGTGCTGTAAgg                                                   >  1:34844787/1‑68 (MQ=14)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                   <  1:11788185/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                   <  1:3464195/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                   <  1:6974847/68‑1 (MQ=255)

          ccTTGCCAAGGGCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                   <  1:4066917/68‑1 (MQ=255)

          ccTGGCCCAGGTCGGGGTCGCGAGTTCGAGGCTCGTTTCCCGCTCCAAACTTTGAAAGTGCTGTAAgg                                                   <  1:16582513/68‑1 (MQ=17)

           cTTGCCAAGGTCTTGGTCGCGAGTTCGAGTCTCGTTTCCCTCTCCAAAATTTGAAAGTGCTGTAAGGc                                                  <  1:19052902/68‑1 (MQ=17)

           cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGc                                                  <  1:23706216/68‑1 (MQ=255)

           cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGc                                                  <  1:1104192/68‑1 (MQ=255)

              gCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGcaca                                               <  1:24158720/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAAGGAACAg                                              >  1:9243785/1‑67 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGATAGTTATGTAAGGaacac                                              >  1:19214542/1‑66 (MQ=14)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                              <  1:15698455/67‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                              >  1:26344790/1‑67 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                              >  1:37647407/1‑67 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                             <  1:29380408/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATATGAAAGAGATGTAAGGAACAg                                              >  1:30143292/1‑67 (MQ=14)

                cAAGGTCGGGGTCGCGAGTTCGAGTCACGTTTCCCGCTCCAAAATTTGCAAGTCCTTTAAGGCCCAg                                              >  1:34295183/1‑67 (MQ=14)

                  aGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGacc                                           <  1:7816431/68‑1 (MQ=255)

                  aGGGCGGGGTCGCGAGTGCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGacc                                           <  1:10485895/68‑1 (MQ=255)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTTAAAGTGATGTAAGGAACAcaccac                                         >  1:26659479/1‑67 (MQ=17)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                         <  1:26942117/67‑1 (MQ=255)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                         >  1:7453912/1‑67 (MQ=255)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                         <  1:25575885/67‑1 (MQ=255)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                         <  1:12273672/67‑1 (MQ=255)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGacca                                          <  1:23449337/66‑1 (MQ=255)

                     tCGGGGGCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                         <  1:25145213/67‑1 (MQ=255)

                         ggTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTTATTTAAGGAACACACCCCCCacg                                    >  1:13172532/1‑66 (MQ=14)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAATGAACAGACCACCCAAGc                                   >  1:17354732/1‑68 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                    <  1:10799219/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                    <  1:18866043/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                    <  1:3197355/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                    <  1:18442584/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                    <  1:7132506/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                    <  1:20514455/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                    <  1:219637/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                    <  1:16220930/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGc                                   >  1:36779699/1‑68 (MQ=255)

                            cgcgAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCgg                                 <  1:29151178/68‑1 (MQ=255)

                            cgcgAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCgg                                 <  1:14991211/68‑1 (MQ=255)

                            cgcgAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCg                                  <  1:11571633/67‑1 (MQ=255)

                             gcgAGTTCGAGGCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCggg                                <  1:8836842/68‑1 (MQ=255)

                               gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                               <  1:18103285/67‑1 (MQ=255)

                               gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                               <  1:1268903/67‑1 (MQ=255)

                               gAGTTCGAGTCTCGTTTCCCGCTCCAAAATATGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                               <  1:28821683/67‑1 (MQ=255)

                                   gcGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGc                          <  1:20725055/67‑1 (MQ=255)

                                       gTCGCGTTTCCCGCGCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                      <  1:10107350/68‑1 (MQ=255)

                                         ctcGTTTCGCGCCCCAAATTTTAAAAGTTCGGTAACCAACAAACCACCCAAGCGGGAATAGCTCAGtt                    <  1:17119983/68‑1 (MQ=9)

                                         ctcGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                      <  1:32595143/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                      <  1:33014123/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                      <  1:17843417/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                      <  1:13485450/66‑1 (MQ=255)

                                         cacGTTTCCCGCGCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                      <  1:38233733/64‑1 (MQ=255)

                                          tcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTg                   <  1:13669008/68‑1 (MQ=255)

                                          tcGTTTCCCCCGCCAAAATTTCAAAGTGCTGTAACTAACAGACCACCCAAGCGGGAATAGCTCAGTTg                   <  1:8515475/68‑1 (MQ=14)

                                           cGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTgg                  >  1:28418051/1‑68 (MQ=255)

                                            gTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGt                 <  1:20620673/68‑1 (MQ=255)

                                               tCCCGCTCCAAAATTTGAAAGTGCTGTAATGCACAGACCACCCAATCGGGAATAGCTCAGTTGGTaga              <  1:3404697/68‑1 (MQ=14)

                                               accccCTACAAAATTTAAAAGTGCTCAAACTCACATACCACCCAAGCGGGAATAGCTCAGTTGGTaga              <  1:6095030/67‑1 (MQ=2)

                                                cccGCTCCAAAATTTGAAAGTGCTGTAAGGCACATACCACCCAAGCGGGAATAGCTCAGTTGGTagag             <  1:33798223/68‑1 (MQ=255)

                                                cccGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga              >  1:20122992/1‑67 (MQ=255)

                                                cccGCTCCAAAATTTCAAAGTGCTGAAACGCACAGACCACCCACGCGGGAATAGCTCAGTTGGTagag             <  1:22302578/68‑1 (MQ=14)

                                                  cGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGc            >  1:5926234/1‑67 (MQ=255)

                                                      ccAAAATTTTAAAGTGCTCTCCGGCACAGACGACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc       <  1:20863940/68‑1 (MQ=17)

                                                      acAAAATTTCAAAGTTCTTAAAGGAACATAACAACCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc       <  1:14299486/67‑1 (MQ=9)

                                                       cAAAATTTTAAATTTCTGTAACGAACATACCAACCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc       <  1:39059476/67‑1 (MQ=14)

                                                          taTTTGAACGTGCTCTATGGCACATACAAACCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTg   <  1:18623765/67‑1 (MQ=14)

                                                          aaTTTTAAATTGCTGTAAGGCACAGAACACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTg   <  1:9665826/68‑1 (MQ=14)

                                                           aTTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCtcg   >  1:22940289/1‑65 (MQ=255)

TAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGC  >  CP009273/4382308‑4382434

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: `‑`