BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,596,120	C→A	7.5%	intergenic (‑17/+12)	leuP ← / ← leuQ	tRNA‑Leu/tRNA‑Leu

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,596,120	0	C	A	7.5%	709.3 / 3.0	256	intergenic (‑17/+12)	leuP/leuQ	tRNA‑Leu/tRNA‑Leu
Reads supporting (aligned to +/- strand): ref base C (157/71); new base A (24/3); total (182/74)
Fisher's exact test for biased strand distribution p-value = 4.13e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 267 total aligned reads displayed.

AAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAA  >  CP009273/4596053‑4596186

aaGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATc                                                                     <  1:16712093/68‑1 (MQ=255)

 aGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCAAGGGCCAGCAATATCa                                                                    >  1:1769919/1‑68 (MQ=17)

  gAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGAGAAGAATATaaa                                                                   >  1:13818058/1‑68 (MQ=14)

    acacTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCGACTGAGAGCAATATAAACg                                                                 >  1:10825959/1‑68 (MQ=14)

    acacTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACg                                                                 >  1:20010032/1‑68 (MQ=255)

    acacTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACg                                                                 <  1:25135469/68‑1 (MQ=255)

    acacTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTCGGAGCAATAACAACg                                                                 >  1:21479132/1‑68 (MQ=14)

    acacTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCAAGTGCGAGCAATATCAACg                                                                 >  1:11140867/1‑68 (MQ=255)

       cTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTgg                                                              <  1:20934583/68‑1 (MQ=255)

         aaCACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGtt                                                            <  1:25447107/68‑1 (MQ=255)

         aaCACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGtt                                                            <  1:3003927/68‑1 (MQ=255)

         aaCACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGtt                                                            <  1:10440043/68‑1 (MQ=255)

            acCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCGAGGGCGAGCAATATCAAAGTGGttatt                                                         >  1:22758768/1‑68 (MQ=18)

            acCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCTATATAAACGTGGttttt                                                         >  1:1912154/1‑68 (MQ=255)

            acCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGttttt                                                         >  1:18186177/1‑68 (MQ=255)

            acCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGttttt                                                         >  1:13730449/1‑68 (MQ=255)

            acCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGttttt                                                         >  1:23485762/1‑68 (MQ=255)

            acCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGAGCTCAATATATAAGTGGtgttt                                                         >  1:17849618/1‑68 (MQ=14)

               tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCTGTGCGAGCAATATCAACGTGGTTTTTGGt                                                      <  1:19624108/68‑1 (MQ=255)

               tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGt                                                      <  1:26382988/68‑1 (MQ=255)

               tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGt                                                      <  1:14295521/68‑1 (MQ=255)

                  aGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCGAGTGCCAGCAATATCAACGTGGTGTTTGGTGCg                                                   >  1:21128182/1‑68 (MQ=25)

                  aGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGTTTTTTGGTGCg                                                   >  1:4827879/1‑68 (MQ=255)

                  aGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGc                                                    <  1:4526424/67‑1 (MQ=255)

                  aGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGc                                                    <  1:11453600/67‑1 (MQ=255)

                  aGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCg                                                   <  1:5040660/68‑1 (MQ=255)

                  aGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGGGCCAGCAATATAAACGTGGTTGTTGGTGCg                                                   >  1:7065792/1‑68 (MQ=21)

                  aGCTAGCGCGTCTACCAATTCCGCCACCTTCGCAGAGTGAGAGAAATATCAACGTGGTTGTAGGTGCg                                                   >  1:1542107/1‑68 (MQ=18)

                  aGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTGGGATGAATATAAACGTGTTGTTTGGTGCg                                                   >  1:14959249/1‑68 (MQ=14)

                    cTAGCGCGTCTACCAATTCCGCCACCTTCGCCGAGAGCGAGGTATATAAACGAGGTGTTTGGTGCGA‑g                                                >  1:6605369/1‑68 (MQ=18)

                    cTAGCGCGTCTACCAATTCCGCCACCTTCGCCCCCAGGGAGCAATATCAACGTGTTGCTTGCTGCGA‑g                                                >  1:27311390/1‑68 (MQ=17)

                    cTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCTATATCAAAGAGGTTTTTCGTCCGA‑g                                                >  1:13148270/1‑68 (MQ=21)

                    cTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑g                                                >  1:14564125/1‑68 (MQ=255)

                    cTAGCGCGTCAACCAATACCGCCACCTTCGCCCAGTGCGAGCAATCTCAACGTGGTTTTTGGTGCGA‑g                                                <  1:1023512/68‑1 (MQ=37)

                     tatcgcgTCTACCAATTCCTCCACCTTCGCCAAGTGCGAGCAATATCAACCTGGTTTTTGGTGCGA‑g                                                <  1:20638626/64‑1 (MQ=37)

                       gcgcGTCTACCAATTCCGCCACCTTCGCCAAGTGCGAGCTATTTCAAAGTGGTGTTTGGTGCGA‑gggg                                             >  1:21599217/1‑68 (MQ=25)

                        cgcgTCTACCAATTCCGCCACCTTCGCCCAGTGGGAGCTATATAAACGTGGTTTTTGGTGCGA‑ggggg                                            >  1:10623986/1‑68 (MQ=37)

                        cgcgTCTACCAATTCCGCCACCTTCGCCCAGTGGGAGCTATATAAAAGTGGTTTTTGGTGCGA‑ggggg                                            >  1:27855547/1‑68 (MQ=25)

                        cgcgTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCTATATCAACGTGGTTTTTGGTGCGA‑ggggg                                            >  1:23000148/1‑68 (MQ=255)

                        cgcgTCTACCAATTCCGCCACCTTCGCCAAGTGCGAGATATATAAACGTGGTTTTTGGTCCGA‑ggggc                                            >  1:790572/1‑67 (MQ=25)

                        cgcgTCTACCAATTCCGCCACCTTCGCACAGAGGGAGCTATATAAACGAGGTGATTGGTGCGA‑ggggc                                            >  1:24538283/1‑67 (MQ=12)

                        cgcgTCTACCAAGTCCGCCACCTTCGCCCAGTGCGAGCTATATCAACGTGGTTTTTGGTCCGA‑ggggg                                            >  1:23728673/1‑68 (MQ=37)

                             cTACCAATTCCGCCCCCTTCGCCCAGTGCTATAAATCTCAACGTGGTTTTTGGTGCGA‑GGGGGGGGa                                        <  1:7815283/67‑1 (MQ=37)

                             cTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGa                                        <  1:2039388/67‑1 (MQ=255)

                             cTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGAc                                       <  1:27697284/68‑1 (MQ=255)

                              tACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATCTCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACt                                      <  1:28963777/68‑1 (MQ=255)

                                 ctaTTCCGAAACCTTCCCCCAGTTCTATCAATATAAACGGGGCTTTTGGTGCGA‑GGGGGGGGACTTGa                                   <  1:25732922/66‑1 (MQ=16)

                                 cAATTCCGCCACCTTCGCCCACTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGa                                   >  1:22838970/1‑68 (MQ=255)

                                 cAATTCCGCCACCATCGCCCAGTCCTAGCAATCTCATCGCGGTTTTTGGTGCGA‑GGGGGGGGACTTGa                                   <  1:1478929/68‑1 (MQ=25)

                                   aTTCCGCCACCTTCTCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGaa                                  >  1:16122939/1‑67 (MQ=255)

                                     tCCGCCACCTTGGCCCAGTGCGAGCATTATCAACGGGGTTTTTGGTGCGA‑GGGGGGGGACTTGAAccc                               <  1:16453460/68‑1 (MQ=37)

                                     tCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAAcc                                >  1:12939459/1‑67 (MQ=255)

                                     tCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAAcc                                >  1:8741024/1‑67 (MQ=255)

                                          cACCTTCGCCCAGTGCTAGAAATATCAACGGGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACg                          <  1:16900164/68‑1 (MQ=25)

                                           aCCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACg                          >  1:24376383/1‑67 (MQ=255)

                                           aCCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACg                          >  1:7645863/1‑67 (MQ=255)

                                           aCCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACg                          >  1:6437196/1‑67 (MQ=255)

                                           aCCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACg                          >  1:6403439/1‑67 (MQ=255)

                                           aCCTTCGCCCAGTGCGAGCAATATCAACGTGGATTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACg                          >  1:21784263/1‑67 (MQ=255)

                                            ccTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGt                         >  1:12416963/1‑67 (MQ=255)

                                             cTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc                       >  1:4107559/1‑68 (MQ=255)

                                             cTTCGCCCAGTCCTAGCAATATCAACGGGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc                       <  1:9722211/68‑1 (MQ=21)

                                               tCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAGGGGGGGGGACTTGAACCCCCACGTCCg                      <  1:18514048/68‑1 (MQ=255)

                                                  cccAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAg                  >  1:1064128/1‑68 (MQ=255)

                                                  cccAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAg                  >  1:20435613/1‑68 (MQ=255)

                                                  cccAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAg                  >  1:17905737/1‑68 (MQ=255)

                                                  cccAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGAATTGACCCCCCCCGACCGTAAg                  >  1:24991036/1‑68 (MQ=25)

                                                   ccAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAgg                 >  1:17508310/1‑68 (MQ=255)

                                                   ccAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAgg                 >  1:2881006/1‑68 (MQ=255)

                                                    ccgTGCTAGCAATATCACCGCGTTTTTTGGGGCGC‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGa                <  1:17075658/66‑1 (MQ=17)

                                                    cAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAgg                 >  1:25959610/1‑67 (MQ=255)

                                                    cAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAgg                 >  1:567455/1‑67 (MQ=255)

                                                     aGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGac               >  1:22594233/1‑68 (MQ=255)

                                                       tGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGac               >  1:24775930/1‑66 (MQ=255)

                                                        gctaGCAATAACAACGGGGCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGaca              <  1:15359886/63‑1 (MQ=17)

                                                        gCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGacac             <  1:8606294/67‑1 (MQ=255)

                                                        gCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGaca              <  1:7376042/66‑1 (MQ=255)

                                                        gCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACt            >  1:3494494/1‑68 (MQ=255)

                                                           aGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAac         >  1:28089542/1‑68 (MQ=255)

                                                             cAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGCCTTGAACCCCCACGTCCGTAAGGACACAAaca        >  1:11881475/1‑67 (MQ=255)

                                                             cAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAaca        >  1:10153113/1‑67 (MQ=255)

                                                             cAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAaca        >  1:20048582/1‑67 (MQ=255)

                                                             cAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAaca        >  1:26482217/1‑67 (MQ=255)

                                                             cAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAaca        >  1:28543183/1‑67 (MQ=255)

                                                             cAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAaca        >  1:18823487/1‑67 (MQ=255)

                                                             cAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAaca        >  1:12697246/1‑67 (MQ=255)

                                                             cAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAaca        >  1:2125769/1‑67 (MQ=255)

                                                             cAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAaca        >  1:3725041/1‑67 (MQ=255)

                                                             cAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAaca        >  1:12234869/1‑67 (MQ=255)

                                                             cAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAaca        >  1:12196058/1‑67 (MQ=255)

                                                             cAATATCAACGTGGTTTATGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAaca        >  1:15928545/1‑67 (MQ=255)

                                                              aacatCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAaca        <  1:5392688/63‑1 (MQ=255)

                                                              aaTATCCAAGTGGTATTTGGTGCGC‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAaca        <  1:4233898/66‑1 (MQ=14)

                                                              aaTATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACAcc      <  1:8575639/68‑1 (MQ=255)

                                                              aaTATCAACGTGCTATTTGGGGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAaca        <  1:15723569/66‑1 (MQ=17)

                                                              aaTAACAACGGGCTTTTTGGGGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAacac       <  1:5893434/67‑1 (MQ=14)

                                                                 atCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGa   >  1:8262871/1‑68 (MQ=255)

                                                                  tCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGaa  >  1:5181488/1‑68 (MQ=255)

                                                                  tCAACGTGGTTTTTGGTGCGA‑‑GGGGGGTACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGaa  >  1:17254094/1‑67 (MQ=17)

                                                                   cAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGaa  >  1:24021683/1‑67 (MQ=255)

AAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAA  >  CP009273/4596053‑4596186

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: `‑`