BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,595,993	T→A	7.4%	intergenic (‑11/+24)	leuV ← / ← leuP	tRNA‑Leu/tRNA‑Leu

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,595,993	0	T	A	7.4%	892.0 / 10.0	314	intergenic (‑11/+24)	leuV/leuP	tRNA‑Leu/tRNA‑Leu
Reads supporting (aligned to +/- strand): ref base T (135/149); new base A (2/24); total (141/173)
Fisher's exact test for biased strand distribution p-value = 4.39e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 355 total aligned reads displayed.

GTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACAC  >  CP009273/4595926‑4596060

  ccGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTa                                                                    <  1:18680248/67‑1 (MQ=255)

    gTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACtt                                                                 <  1:21418409/68‑1 (MQ=255)

      aaGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTGCttt                                                                <  1:26526499/67‑1 (MQ=255)

      aaGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACttt                                                                <  1:21724914/67‑1 (MQ=255)

      aaGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACttt                                                                <  1:41969683/67‑1 (MQ=255)

      aaGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACttt                                                                <  1:26286055/67‑1 (MQ=255)

      aaGGACACTAACACCTGAAGCTAGCGCGTCTACCAAATCCGCCACCTTCGCACAGTCATCTTACtttt                                                               >  1:14549622/1‑68 (MQ=255)

       aGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACttttt                                                              >  1:1531652/1‑68 (MQ=255)

       aGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTAAGCTTTCttttt                                                              >  1:25559030/1‑68 (MQ=14)

        ggACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCAGCTTACtttatt                                                             >  1:23276719/1‑68 (MQ=255)

            acTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGat                                                         <  1:40548570/68‑1 (MQ=255)

                acacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCg                                                     <  1:34886478/68‑1 (MQ=255)

                 cacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGc                                                    <  1:6467040/68‑1 (MQ=255)

                 cacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGc                                                    <  1:39124937/68‑1 (MQ=255)

                  acCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCAGAGACAGCTTTCTTTTTAAGATATCgtc                                                   >  1:19967161/1‑66 (MQ=14)

                  acCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATATTAATATATTTGatatag                                                     >  1:15620480/1‑64 (MQ=17)

                     tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                <  1:24598528/68‑1 (MQ=255)

                     tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                <  1:19261344/68‑1 (MQ=255)

                     tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                <  1:17139616/68‑1 (MQ=255)

                     tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                <  1:30260944/68‑1 (MQ=255)

                     tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                <  1:23496516/68‑1 (MQ=255)

                      gAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGt                                               <  1:5886750/68‑1 (MQ=255)

                        aGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGtt                                              <  1:17716351/67‑1 (MQ=255)

                        aGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGgtt                                             >  1:14090392/1‑68 (MQ=255)

                        aGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGGCTCATTACTTTTATTGATATGGGCTCggtg                                             >  1:5259858/1‑65 (MQ=17)

                          cTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATTTCGCCTCGTTggg                                           >  1:37164295/1‑68 (MQ=255)

                           tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTgg                                           <  1:41022482/67‑1 (MQ=255)

                           tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTg                                            <  1:38678300/66‑1 (MQ=255)

                           tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                          <  1:34187673/68‑1 (MQ=255)

                           tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                          <  1:10871744/68‑1 (MQ=255)

                           tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                          <  1:38954486/68‑1 (MQ=255)

                           tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                          <  1:35686102/68‑1 (MQ=255)

                           tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                          <  1:43402848/68‑1 (MQ=255)

                           tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                          <  1:28326919/68‑1 (MQ=255)

                           tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                          <  1:12419423/68‑1 (MQ=255)

                           tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                          <  1:33897983/68‑1 (MQ=255)

                           tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                          <  1:16035116/68‑1 (MQ=255)

                           tAGCCCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                          <  1:19021408/68‑1 (MQ=255)

                               gcgTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGa                                      <  1:35904793/68‑1 (MQ=255)

                                 gTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAg                                     <  1:21153616/67‑1 (MQ=255)

                                 gTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAg                                     <  1:41773916/67‑1 (MQ=255)

                                 gTCTACCAATTCCGCCACCTTCGCACAGGCATCTTACATTTTTTGATATCGCCTCGTTTGGTGCGAg                                     <  1:10006937/67‑1 (MQ=38)

                                   cTACCAATTCCGCCACCTTCTCACAGTCATCTTACTTTTTTTGATATCCCCTCGTTTGGTGCGAggg                                   <  1:9067899/67‑1 (MQ=39)

                                   cTACCAATTCCGCCACCTTCTCACAGTCATCATACATTTTTTGATATCGCCTCTTTTGGTGCGAggg                                   <  1:5606347/67‑1 (MQ=38)

                                   cTACCAATTCCGCCACCATCGCACAGTCATCTTACTTTATTTGATATCGCCTCGTTTGGTGCGAggg                                   <  1:20877619/67‑1 (MQ=39)

                                       cAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAgggggggg                              >  1:32930355/1‑68 (MQ=255)

                                         aTTCCGCCACCATATCACAGTCATCTTACTTTTTTTGATATCGCCTCCTTTGGTGCGAGGGGGGGGAc                            <  1:37452342/68‑1 (MQ=38)

                                          ttCCGCCACCATCGCACACTCATCATACATTTTTTGAAATCCCCACGTTTGGTGCGAGGGGGGGGACt                           <  1:5054025/68‑1 (MQ=25)

                                           tCCGCCACCTTCGCACAGTCATCTTAATTTTATTGATTTCGCCTCGAGAGGTGCGCGGGGGGGGACtt                          >  1:34733744/1‑68 (MQ=255)

                                           tCCGCCACCTTCGCACAGTCATATTTCTTTTTTTGATATCGCATCGTTTGGTGCGAGGGGGGGGACtt                          >  1:39415611/1‑68 (MQ=38)

                                           tCCGCCACCTTCGCACAGTCAGCTTACTTTTTTTGATATCGCCGCGTTTGGTGCGAGGGGGGGGACtt                          >  1:23608761/1‑68 (MQ=39)

                                                cACCTTCGCACAGGCATCTTACTTTTATTGAAATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAAcc                     <  1:11993990/68‑1 (MQ=37)

                                                 acattCGCACAGTCATATTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGAATTGAAcc                     >  1:29231422/4‑67 (MQ=38)

                                                 aacTTCGCACAGTCATCAAACTTTTATTGAAATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAAccc                    <  1:24083552/66‑1 (MQ=25)

                                                 aCCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAAcc                     >  1:25424197/1‑67 (MQ=255)

                                                 aCCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGGTTGGTGCGAGGGGGGGGACTTGAAcc                     >  1:12967396/1‑67 (MQ=255)

                                                 aCCTTCGCACAGTCATCATACTTAATTTGATATCGCCTCGTTTGGTGCGAGGCGGGGGACTTGCAcc                     >  1:11784361/1‑67 (MQ=255)

                                                  ccTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCTTTTGGTGCTAGGGGGGGGACTTCAAacc                    >  1:4874968/1‑67 (MQ=38)

                                                       taacaGTCATCTAACTTTTTTTGAATTCCCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGt              <  1:3197115/66‑1 (MQ=21)

                                                       cctcaGGCATCTAACTTTTTTTGATATCCCCTCTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGt              <  1:3685803/65‑1 (MQ=18)

                                                        cacaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGt              >  1:2209902/1‑67 (MQ=255)

                                                        cacaGGCATCAAACTTTATATGATATCGCCACGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTc             <  1:608861/68‑1 (MQ=18)

                                                        aacaGTGATCTTACATTTTTTGAAATCCCGTTTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTc             <  1:16596857/67‑1 (MQ=14)

                                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGCACCCCCACGTcc            >  1:22889852/1‑68 (MQ=255)

                                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc            >  1:38809184/1‑68 (MQ=255)

                                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc            >  1:25495055/1‑68 (MQ=255)

                                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc            >  1:34384025/1‑68 (MQ=255)

                                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc            >  1:33169966/1‑68 (MQ=255)

                                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc            >  1:30646197/1‑68 (MQ=255)

                                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc            >  1:20961347/1‑68 (MQ=255)

                                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc            >  1:43020144/1‑68 (MQ=255)

                                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc            >  1:25969710/1‑68 (MQ=255)

                                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACACCCACGTcc            >  1:13509909/1‑68 (MQ=255)

                                                         acaGTCATCTAACTATATTTGAAATACCCACGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc            <  1:20500428/68‑1 (MQ=17)

                                                           aGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGt          >  1:2376616/1‑68 (MQ=255)

                                                            ttCATCTTACATTTTTTGAAATACCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTa         <  1:10252563/67‑1 (MQ=18)

                                                            gccATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTa         >  1:42797798/3‑68 (MQ=255)

                                                            gTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTa         >  1:13804145/1‑68 (MQ=255)

                                                             tCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTaa        >  1:38350365/1‑68 (MQ=255)

                                                             tCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTaa        >  1:4520237/1‑68 (MQ=255)

                                                             tCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGAATTGAACCCCCACGTCCGTaa        >  1:11073856/1‑68 (MQ=255)

                                                              catcatACTTTTTTTGATATATCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTa         <  1:6532610/66‑1 (MQ=18)

                                                              cATCTTCCTTTTTTTTTTATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCg           <  1:8052089/64‑1 (MQ=18)

                                                              cATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTa         <  1:10622355/66‑1 (MQ=255)

                                                              cATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAg       >  1:19603101/1‑68 (MQ=255)

                                                              cATCTTACTTTTTATGATATCGCCTCCTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTaa        <  1:31211524/67‑1 (MQ=255)

                                                              cATCTAACATTTTTTGATTTCCCCTCTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTa         <  1:28881870/66‑1 (MQ=17)

                                                              cATCTAACATTTTTTGATCTCCCCTCTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAg       <  1:36259779/68‑1 (MQ=17)

                                                               aTCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGa      <  1:2803286/68‑1 (MQ=255)

                                                               aTCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGa      <  1:12349407/68‑1 (MQ=255)

                                                               aTCTTAATTTTTTTGATAACGCCTCGTTTGGTGCGA‑GGGGGGGACTTGAACCCCCACGTCCGTAAGaa     <  1:42481244/68‑1 (MQ=21)

                                                               aTCTAACTTTATTTGATTTACCCTAGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGa      <  1:32279616/68‑1 (MQ=14)

                                                                acTTACTTTTTTTGATATCGCCTCTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGaa     <  1:30495021/67‑1 (MQ=255)

                                                                  ttACTTTTTTTGATATCGCCTGGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAaca   <  1:16244252/68‑1 (MQ=255)

                                                                  ttACTTTTTTTGATATCGCCTCGTTTGGTGCGCGGGGGGGGACTTGAACCCCCACGTCCGTAAGAaca   <  1:11290770/68‑1 (MQ=255)

                                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:22360167/1‑66 (MQ=255)

                                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:31510194/1‑66 (MQ=255)

                                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:31820044/1‑66 (MQ=255)

                                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:733078/1‑66 (MQ=255)

                                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:33664884/1‑66 (MQ=255)

GTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACAC  >  CP009273/4595926‑4596060

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: `‑`