BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,382,371	G→T	8.7%	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	8.7%	841.5 / 6.4	315	intergenic (+7/‑29)	glyX/glyY	tRNA‑Gly/tRNA‑Gly
Reads supporting (aligned to +/- strand): ref base G (72/198); new base T (14/19); total (86/229)
Fisher's exact test for biased strand distribution p-value = 6.69e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 315 total aligned reads displayed.

TAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTG  >  CP009273/4382308‑4382433

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTTAAAg                                                            >  1:16467481/1‑68 (MQ=255)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAg                                                            >  1:13016535/1‑68 (MQ=14)

 tgagCACGACCTTGCCTTTGTCGTGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                           <  1:14939432/67‑1 (MQ=11)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                           <  1:28971681/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                           <  1:4890388/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                           <  1:8066663/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                           <  1:7951270/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                           <  1:12148700/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                           <  1:24310267/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATATGAAAGt                                                           <  1:15565006/68‑1 (MQ=18)

 agagCACGACCTTGCCAAGGGCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                           <  1:1817291/68‑1 (MQ=18)

    gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGc                                                         <  1:22411963/67‑1 (MQ=37)

    gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGc                                                         <  1:17264973/67‑1 (MQ=37)

    gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGc                                                         <  1:23443091/67‑1 (MQ=37)

    gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGc                                                         <  1:9912446/67‑1 (MQ=37)

    gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCt                                                        >  1:19103023/1‑68 (MQ=39)

      tcGAGCTTGGCATGGTAGTGGTCGATATTTCTATTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCt                                                        <  1:23550157/65‑1 (MQ=9)

      aCGACCTTGCCAAGGTCGGGGTCGCGTGTTCGAGTCTCGTTTACCGCTCCAAAATTTTAAAGTGCTga                                                      >  1:21869715/1‑67 (MQ=14)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTGAAAGTGATGt                                                      >  1:29184855/1‑68 (MQ=255)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCt                                                        <  1:12445220/66‑1 (MQ=39)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:26808268/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:1927006/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:25650927/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:20996162/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      >  1:15424578/1‑68 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:2300260/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:15104433/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:10992299/68‑1 (MQ=40)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGCTTTaat                                                   >  1:20383474/1‑67 (MQ=14)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGATGTAAg                                                   >  1:28362497/1‑68 (MQ=255)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGATAGAGCTGTAAg                                                   >  1:6349149/1‑68 (MQ=255)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAg                                                   >  1:10872226/1‑68 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                  <  1:16193718/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                  <  1:21184058/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                  <  1:21317043/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                  <  1:24518842/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                  <  1:24992675/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                  <  1:13366568/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                  <  1:28696083/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                  <  1:22497927/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAg                                                   >  1:18008266/1‑67 (MQ=255)

           cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGc                                                 <  1:8857179/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTGAAAGTGCTGTAAGGAACAg                                             >  1:23825791/1‑67 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                             >  1:2489643/1‑67 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                             <  1:16912351/67‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                            <  1:18993482/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                            <  1:14973984/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                            <  1:15248402/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGATGTAAGGAACAg                                             >  1:7722577/1‑67 (MQ=255)

                cAAGGTCGGGGTCGCGAGGTCGAGGCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                            <  1:20170652/68‑1 (MQ=255)

                  aGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGacc                                          <  1:18445485/68‑1 (MQ=255)

                  aGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGacc                                          <  1:12642447/68‑1 (MQ=255)

                    gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTTTAAGGCACAGaccc                                         >  1:21945675/1‑66 (MQ=255)

                    gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGTCACAGaccc                                         >  1:23375856/1‑66 (MQ=255)

                    gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCCCACaccc                                         >  1:25829983/1‑66 (MQ=17)

                    gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGATGTAATGCCCAGaccg                                         >  1:25991884/1‑66 (MQ=14)

                    gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGAGCTGTAAGGCACACacca                                         >  1:13779663/1‑67 (MQ=255)

                    gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATATGAAAGAGATGTAATGAACAGaccc                                         >  1:15311813/1‑66 (MQ=14)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAAGGCACAGaccac                                        >  1:1732553/1‑67 (MQ=255)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                        <  1:26476615/67‑1 (MQ=255)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGacca                                         <  1:22196521/66‑1 (MQ=255)

                      ggcggTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccacc                                       <  1:27493068/64‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTGAAAGTGCTGTAAGGGACAGACCGCCCAAgg                                  >  1:14501238/1‑67 (MQ=17)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAATTGCTTTAAGGCACAGACCACCCAAGc                                  >  1:21802959/1‑68 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:3160397/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:5600465/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:11341827/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:4532548/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:3403875/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:19239242/67‑1 (MQ=255)

                            cgcgAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCg                                 <  1:9390331/67‑1 (MQ=255)

                             gcgAGTTCGAGTCTCGTTTCCCGCGCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCggg                               <  1:27944589/68‑1 (MQ=255)

                               ttgTTCGTGGCTCGTTTACCGCTCCAAAATTTGAAAGTGCTGTAATGCACAGACCACCCAAGCGGGa                              <  1:7645229/65‑1 (MQ=14)

                               gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                              <  1:9013678/67‑1 (MQ=255)

                               gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                              <  1:3849151/67‑1 (MQ=255)

                               gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                              <  1:9161362/67‑1 (MQ=255)

                               gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAACGCACAGACCACCCAAGCGGGa                              <  1:17196846/67‑1 (MQ=255)

                                   tCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATa                           <  1:6154479/66‑1 (MQ=255)

                                       ggctcGTTTCCGGGTCCAAATTTTCAAAGTGCTGTAACTCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:10423604/66‑1 (MQ=14)

                                       gTCTCGTTTCCCGCTCCAAAATTTTAACGATATGTAAGCAACAGACCACCCCACCGGGAATAGCTAAg                     >  1:5736453/1‑68 (MQ=12)

                                       gTCTCGTTTCCCGCTCCAAAATATGAAAGAGCTGTAATGCACACACCCCCGAATCGCGAATAGc                         >  1:13932454/1‑64 (MQ=9)

                                       gTCTCGTTTCCCGCGCCAAAATTTGAAAGTGCTGAAACGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:4289482/68‑1 (MQ=14)

                                       gTCTCGTTTCCAGCGCCAAAATTTGAAAGTGCTGTATGGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:3338817/68‑1 (MQ=17)

                                        tctcGTTTCCCGCTCCAAAATTTTATATATCTCTAATACACAGACCACCCAACCCGGAATAGCTCAga                    >  1:11289516/1‑67 (MQ=9)

                                         ctcGTTTCCCGCTCCAAATTTTGAAAGTTCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:7472875/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTTAAAGTTCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:12039371/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:9610957/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:10411527/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGt                    <  1:10040464/67‑1 (MQ=255)

                                         ctcGTTTCCCGCCCAAAAATTTTAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGtt                   <  1:6618446/68‑1 (MQ=17)

                                         ctcGTTACCCGCGCCAAAATTTGAAATTGCTGTAAGGCACAGACCACGCAAGCGGGAATAGCTCAg                     <  1:12911922/66‑1 (MQ=17)

                                            gTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGt                <  1:27823034/68‑1 (MQ=255)

                                              ttCCCGCTCCAAAATTTGAAAGTGCTGTAAGCCACAGACCACCCCAGCGGGAATAGCTCAGTTGGTag              >  1:5369349/1‑68 (MQ=255)

                                                cgcGCTCCAAAATTTGAAAGTGCTGTAAGGCACATACCACGCAAGCGGGAATAGCTCAGTTGGTagag            <  1:13120879/66‑1 (MQ=17)

                                                cccGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga             >  1:19496404/1‑67 (MQ=255)

                                                    cTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACg        >  1:20774853/1‑68 (MQ=255)

                                                     cccAAAATTTTAAAGTGCTTTAAGGCACATACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGa       <  1:2057468/67‑1 (MQ=17)

                                                      ccAAATTATCAAATTGCTGAACGGCACATACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc      <  1:8025497/68‑1 (MQ=11)

                                                      ccAAAATTTTAAAGTGCGTAAAGTCACATACCACCAAAGCGGGAATAGCTCAGTTGGTAGAGCACGa       <  1:5987495/67‑1 (MQ=14)

                                                           aTTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTg  >  1:17569964/1‑67 (MQ=255)

TAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTG  >  CP009273/4382308‑4382433

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: `‑`