BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,596,009	G→C	15.8%	intergenic (‑27/+8)	leuV ← / ← leuP	tRNA‑Leu/tRNA‑Leu

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,596,009	0	G	C	15.8%	811.4 / 41.6	328	intergenic (‑27/+8)	leuV/leuP	tRNA‑Leu/tRNA‑Leu
Reads supporting (aligned to +/- strand): ref base G (140/122); new base C (4/50); total (145/183)
Fisher's exact test for biased strand distribution p-value = 4.40e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 331 total aligned reads displayed.

ACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTA  >  CP009273/4595942‑4596075

 cacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGc                                                                   <  1:10633957/68‑1 (MQ=255)

 cacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGc                                                                   <  1:3554219/68‑1 (MQ=255)

 cacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGc                                                                   <  1:3093984/68‑1 (MQ=255)

     tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                               <  1:33290888/68‑1 (MQ=255)

     tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                               <  1:18546443/68‑1 (MQ=255)

          cTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATAGCATCGTTTgg                                                          >  1:14676870/1‑68 (MQ=255)

           tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTgg                                                          <  1:31112662/67‑1 (MQ=255)

           tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                                         <  1:10600805/68‑1 (MQ=255)

           tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                                         <  1:22110978/68‑1 (MQ=255)

           tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                                         <  1:19793005/68‑1 (MQ=255)

           tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                                         <  1:31273565/68‑1 (MQ=255)

             gcgcGTCTACCAATTCCGCCACCTTCGCACAGGCAGATTACTTTATTAGATATCGGAACGTTGGGTGc                                                       >  1:1882440/1‑68 (MQ=12)

               gcgTCTACCAATTCCGCCACCTTCGCACAGTCATCTGACTTTTTTTGATATCGACTCGTTTGGTGCGa                                                     >  1:38824929/1‑68 (MQ=255)

                 gTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAg                                                    <  1:697102/67‑1 (MQ=255)

                   cTACCAATTCCGCCACCTTCGCACATTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAgggg                                                 <  1:11648909/68‑1 (MQ=255)

                   cTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAggg                                                  <  1:18302810/67‑1 (MQ=255)

                   cTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAggg                                                  <  1:25006828/67‑1 (MQ=255)

                   cTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAggg                                                  <  1:25049888/67‑1 (MQ=255)

                   cTACCAATTCCGCCACCATCGCACATTCATCTAACTTTTTTTGATATCCCCTCGTTTGGTGCGAgggg                                                 <  1:29817952/68‑1 (MQ=38)

                     aCCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAgggggg                                               >  1:32404172/1‑68 (MQ=255)

                         aatCCGCCACCAACGCACAGGCATCTTACATTTTTTGAAATCGCCTCTATTGGTGCGAGGGGGGGGAc                                           <  1:22463922/66‑1 (MQ=25)

                         aTTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGACTCGTTTGGTGCGAgggggggg                                             >  1:20177235/1‑66 (MQ=255)

                          ttCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGTGGGACt                                          >  1:2180521/1‑68 (MQ=255)

                          ttCCGCCACCTTCGCACAGTCATATTACTTTTTTTGATTTGGCCGCGGGGGGTGCGAGGGGGGGGCCt                                          >  1:15205357/1‑68 (MQ=255)

                           tCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACtt                                         >  1:292256/1‑68 (MQ=255)

                           tCCGCCACCTTCGCACAGTCATATTACTTTATTTGATATCGCCTCGTTTGGTGCGAGGGGTGGGACtt                                         >  1:3063447/1‑68 (MQ=39)

                           tCCGCCACCTTCGCACAGTCAGCTGACTTTTTTAGATTTCGCCTAGTTTGGTCAGAGGGGGGGGGCtt                                         >  1:17981622/1‑68 (MQ=255)

                           tCCGCCACCAACCCACAGTCAACATACTTTTATTGAAATCCCCTCCATTGGTGCGAGGGGGGGGACtt                                         <  1:4966851/68‑1 (MQ=16)

                             cGCCACCAACGAACACTCATCATACTTTTTTTGAAATCCCCTCTTTTGGTGCGAGGGGGGGGACTTGa                                       <  1:37333509/68‑1 (MQ=18)

                                 aCCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAAcc                                    >  1:12220169/1‑67 (MQ=255)

                                 aCCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAAcc                                    >  1:28289004/1‑67 (MQ=255)

                                 aCCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAAcc                                    >  1:33529504/1‑67 (MQ=255)

                                 aCCTTCGCACAGTCATCTTACTTTTTTTGAAATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAAccc                                   <  1:13257913/68‑1 (MQ=255)

                                 aCCTTCGAACAGTCATCTTACATTTTTTGATCTCGCCTCTTTTGGTGCGAGGGGGGGGACTTGAAccc                                   <  1:21598939/68‑1 (MQ=25)

                                 aCCATCCCACATTCATCTAACTATATTTGATCTCCCCTCCTTTGGTGCGAGGGGGGGGACTTGAAccc                                   <  1:22219851/68‑1 (MQ=12)

                                       gCACAGTCATCTAACTATTTTTGATATCGCCTCTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGt                             <  1:27702198/68‑1 (MQ=21)

                                       gCACAGTCATCATACTTTTTTTGATATCGCCTCCTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGt                             <  1:37386433/68‑1 (MQ=255)

                                       ccacaGTAATCAAACATTATTTGATATCCCCTCTTTTGGGGCGCGGGGGGGGACTTGAACCCCCACGt                             <  1:26673456/67‑1 (MQ=12)

                                       ccacaGGCATCATACATTATTTGATATCCCCTCTTTTGGGGCGAGGGGGGGGACTTGAACCCCCACGt                             <  1:5850836/67‑1 (MQ=17)

                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGCGGGGGGGGACTTGAAACCCCACGTcc                           >  1:31436135/1‑68 (MQ=255)

                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGACCCCCCACGTcc                           >  1:20348584/1‑68 (MQ=255)

                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGt                             >  1:6383941/1‑66 (MQ=255)

                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc                           >  1:3254311/1‑68 (MQ=255)

                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc                           >  1:8573764/1‑68 (MQ=255)

                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc                           >  1:31714614/1‑68 (MQ=255)

                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc                           >  1:7960462/1‑68 (MQ=255)

                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc                           >  1:14058021/1‑68 (MQ=255)

                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc                           >  1:27396613/1‑68 (MQ=255)

                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc                           >  1:4193817/1‑68 (MQ=255)

                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc                           >  1:17343541/1‑68 (MQ=255)

                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc                           >  1:37144758/1‑68 (MQ=255)

                                           aGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGt                         >  1:10004581/1‑68 (MQ=255)

                                           aGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGt                         >  1:30428892/1‑68 (MQ=255)

                                            gTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTa                        >  1:13577822/1‑68 (MQ=255)

                                             tCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTaa                       >  1:36277313/1‑68 (MQ=255)

                                              catcatACTTTTTTTGATCTCGCCTCTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCg                          <  1:15901980/64‑1 (MQ=18)

                                              cATCTAACTTTTTTTGAACTCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTa                        <  1:24356932/66‑1 (MQ=18)

                                              cATCTAACTTTATTTGATATACCCTCTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCg                          <  1:35309692/64‑1 (MQ=17)

                                                tCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGaa                    <  1:12523198/68‑1 (MQ=255)

                                                 cTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTAGAACCCCCACGTCCGTAAGAac                   >  1:14772902/1‑68 (MQ=255)

                                                  ttACTTTTTTTGATATCGCCTCTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAaca                  <  1:14405255/68‑1 (MQ=255)

                                                  atACTTTTTTTGATATCCCGTCGATTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAaca                  <  1:12754322/67‑1 (MQ=18)

                                                  atACTATTATTGATATCCCCTCTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAaca                  <  1:18225856/67‑1 (MQ=17)

                                                  aaaCTTTTTTTGATATCCCCAAATTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAaca                  <  1:16656689/66‑1 (MQ=17)

                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAccac                 >  1:16173782/1‑68 (MQ=255)

                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac                   >  1:6658714/1‑66 (MQ=255)

                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac                   >  1:36311379/1‑66 (MQ=255)

                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac                   >  1:27597202/1‑66 (MQ=255)

                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac                   >  1:25857778/1‑66 (MQ=255)

                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac                   >  1:16467580/1‑66 (MQ=255)

                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac                   >  1:17088623/1‑66 (MQ=255)

                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac                   >  1:13833486/1‑66 (MQ=255)

                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac                   >  1:21050425/1‑66 (MQ=255)

                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac                   >  1:30097686/1‑66 (MQ=255)

                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac                   >  1:30825770/1‑66 (MQ=255)

                                                   tACTTTTTTTGATATCCCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac                   >  1:6157931/1‑66 (MQ=255)

                                                   tACTTTTTTTGATATCCCCTCCTTTGGTTCGA‑GTGGGGGACTTGAACGACCACGTCCGTAAGAACACt                >  1:35135795/1‑68 (MQ=18)

                                                   aaCTTTTTTTGAAATCTCCATTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAacac                 <  1:36644520/67‑1 (MQ=14)

                                                    aCTTTTTTTGATTTAGCCTCGTTTGGGGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACt                <  1:12836818/68‑1 (MQ=18)

                                                    aCTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACt                <  1:8974169/68‑1 (MQ=255)

                                                     cTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTa               >  1:1104540/1‑68 (MQ=255)

                                                      tttttttGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTa               >  1:8858741/1‑67 (MQ=255)

                                                       ttttttGATACCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAac             >  1:3800364/1‑68 (MQ=255)

                                                        tttttGATATCGCCTGGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAaca            <  1:26171049/68‑1 (MQ=255)

                                                        tttttGATATCGCCTGGGTTGGTGGGTGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAaca            <  1:15459181/68‑1 (MQ=18)

                                                        ttattGAAATAGACTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAaca            <  1:7218761/65‑1 (MQ=14)

                                                         ttttGAAATCTCCTCTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAacac           <  1:17874416/68‑1 (MQ=14)

                                                          tttGATATCGCGTGGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACAcc          <  1:32114527/68‑1 (MQ=255)

                                                          tttGATATCGCCTAGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACAcc          <  1:38211925/68‑1 (MQ=255)

                                                          tttGATATCCCCTGTTTTGGGGCGTGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACAcc          <  1:23484860/68‑1 (MQ=14)

                                                          tttGATATAGCCTCTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACAcc          <  1:12866826/68‑1 (MQ=255)

                                                          tttGATATACCCTCCTCTGGGGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACAcc          <  1:9498584/68‑1 (MQ=14)

                                                          tttGAAATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACAcc          <  1:26303396/68‑1 (MQ=255)

                                                            tGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTg        >  1:5070072/1‑68 (MQ=255)

                                                               tataGCCTCCTTTGGTGCGTGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGaa      <  1:34881922/67‑1 (MQ=14)

                                                               aatCCCCTCTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGaa      <  1:19391863/66‑1 (MQ=14)

                                                               aatCCCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGaa      <  1:32994246/66‑1 (MQ=11)

                                                                atCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGaa      >  1:4561704/1‑66 (MQ=255)

                                                                atCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGaa      >  1:28563795/1‑66 (MQ=255)

                                                                   gCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTa  >  1:8437546/1‑67 (MQ=255)

ACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTA  >  CP009273/4595942‑4596075

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`