BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AP009048	3,920,280	A→T	8.7%	D29E (GAT→GAA)	cspA ←	major cold shock protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AP009048	3,920,280	0	A	T	8.7%	250.1 / 14.5	92	D29E (GAT→GAA)	cspA	major cold shock protein
Reads supporting (aligned to +/- strand): ref base A (44/40); new base T (2/6); total (46/46)
Fisher's exact test for biased strand distribution p-value = 2.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.50e-01

Only 100 of 110 total aligned reads displayed.

AGGACACTTTCTGACCTTCGTCCAGAGATTTGTAACCATCGTTCTGGATAGCAGAGAAGTGTACGAACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATAC  >  AP009048/3920210‑3920347

cagtccggaacaatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcacaca                                                                     >  1:4421178‑M2/67‑71 (MQ=255)

cagtccggaacaatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcacaca                                                                     >  1:421003‑M2/67‑71 (MQ=255)

 agtccggaacaatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcacaca                                                                     <  1:398208‑M2/5‑1 (MQ=255)

 agtccggaacaatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACAt                                                                    <  1:1716109‑M2/6‑1 (MQ=255)

  gtccggaacaatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACTTc                                                                   <  1:5266371‑M2/7‑1 (MQ=255)

   tccggaacaatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACTtcg                                                                  <  1:3245275‑M2/8‑2 (MQ=255)

   tccggaacaatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACTtcg                                                                  <  1:647834‑M2/8‑2 (MQ=255)

   tccggaacaatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACTtcg                                                                  <  1:4971532‑M2/8‑2 (MQ=255)

    ccggaacaatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACTtcg                                                                  <  1:5075723‑M2/8‑2 (MQ=255)

     cggaacaatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACActtcggt                                                                <  1:874552‑M2/10‑4 (MQ=255)

     cggaacaatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACActtcggt                                                                <  1:322044‑M2/10‑4 (MQ=255)

     cggaacaatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACActtcggt                                                                >  1:3526818‑M2/62‑68 (MQ=255)

     cggaacaatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACActtcggt                                                                >  1:182662‑M2/62‑68 (MQ=255)

     cggaacaatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACActtcggt                                                                >  1:4585795‑M2/62‑68 (MQ=255)

     cggaacaatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACttcgg                                                                 <  1:3138113‑M2/9‑3 (MQ=255)

     cggaacaatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCttt                                                                <  1:1414664‑M2/10‑1 (MQ=255)

      ggaacaatttgaaaacaagaacctcgcttaggcctgtgtccatattacgttggtaggatcACACATCTTTa                                                               <  1:4049435‑M2/11‑1 (MQ=255)

       gaacaatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCttt                                                                <  1:863112‑M2/10‑1 (MQ=255)

         acaatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTagag                                                            >  1:228228‑M2/58‑71 (MQ=255)

         acaatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTagag                                                            >  1:2442385‑M2/58‑71 (MQ=255)

          caatttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGc                                                           <  1:3703618‑M2/15‑1 (MQ=255)

             tttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCAt                                                        <  1:4298220‑M2/18‑1 (MQ=255)

             tttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCAt                                                        >  1:3491602‑M2/54‑71 (MQ=255)

             attgaaaacaagaaactcgcttaggcctgtgtccatattacgtgggtaggatcACACTtcg                                                                  >  1:1724077‑M2/54‑60 (MQ=255)

              ttgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATc                                                       >  1:4378143‑M2/53‑71 (MQ=255)

               tgaaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACTtcg                                                                  >  1:5325210‑M2/52‑58 (MQ=255)

                 aaaacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGt                                                     <  1:1917026‑M2/21‑1 (MQ=255)

                   aacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAg                                                  >  1:787728‑M2/48‑71 (MQ=255)

                   aacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAg                                                  >  1:2710709‑M2/48‑71 (MQ=255)

                   aacaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAg                                                  >  1:3220334‑M2/48‑71 (MQ=255)

                    acaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATc                                                       <  1:1957775‑M2/19‑1 (MQ=255)

                    acaagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAgg                                                 <  1:334929‑M2/25‑1 (MQ=255)

                      aagaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAg                                               <  1:725741‑M2/27‑1 (MQ=255)

                       agaacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGt                                              <  1:319166‑M2/28‑1 (MQ=255)

                         aacctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTag                                                              <  1:105902‑M2/12‑1 (MQ=255)

                          acctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGtgat                                           <  1:810580‑M2/31‑1 (MQ=255)

                           cctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTATAGCCATCGTCAGGAGtgatg                                          <  1:68234‑M2/32‑1 (MQ=255)

                            ctcgcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGt                                                     <  1:1086648‑M2/21‑1 (MQ=255)

                             tcgcttaggcctgtgtccatattacgtgtgtaggatcAAACATCTTTAGAGCCATCGTCAgg                                                 >  1:5113840‑M2/38‑62 (MQ=255)

                             tcgcttaggcctgtgtccatattacgtgggtaggatcACACATCttt                                                                >  1:3727846‑M2/38‑47 (MQ=255)

                               gcttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaa                                        <  1:4049345‑M2/34‑1 (MQ=255)

                                cttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGtgatg                                          <  1:4998035‑M2/32‑1 (MQ=255)

                                 ttaggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaagcc                                     >  1:5053051‑M2/34‑70 (MQ=255)

                                   aggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCg                                                      <  1:3584869‑M2/20‑1 (MQ=255)

                                   aggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGAtgaagccc                                    >  1:2225822‑M2/32‑68 (MQ=255)

                                   aggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaagccga                                   <  1:4272189‑M2/39‑1 (MQ=255)

                                   aggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaagccg                                    <  1:2599881‑M2/38‑1 (MQ=255)

                                   aggcctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaagccg                                    <  1:416569‑M2/38‑1 (MQ=255)

                                      cctgtgtccatattacgtgggtaggatcACACATCTTTa                                                               <  1:3311720‑M2/11‑1 (MQ=255)

                                      cctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaagccgaagcc                               <  1:2676128‑M2/43‑1 (MQ=255)

                                       ctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTc                                                    >  1:73216‑M2/28‑49 (MQ=255)

                                       ctgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCt                              >  1:1044736‑M2/28‑71 (MQ=255)

                                        tgtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCtt                             >  1:2840136‑M2/27‑71 (MQ=255)

                                         gtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCttt                            >  1:2485057‑M2/26‑71 (MQ=255)

                                         gtgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCtt                             >  1:1145231‑M2/26‑70 (MQ=255)

                                          tgtccatattacgtgggtaggatcACACATCTTTa                                                               >  1:230550‑M2/25‑35 (MQ=255)

                                          tgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAg                                                  >  1:424641‑M2/25‑48 (MQ=255)

                                          tgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaag                                       >  1:4743838‑M2/25‑59 (MQ=255)

                                          tgtccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaag                                       >  1:4570903‑M2/25‑59 (MQ=255)

                                            tccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGt                                              <  1:3622634‑M2/28‑1 (MQ=255)

                                            tccatattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGt                          <  1:2763457‑M2/48‑1 (MQ=255)

                                              catattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGtgatga                                         <  1:2907801‑M2/33‑1 (MQ=255)

                                              catattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaagccgaag                                 >  1:2809626‑M2/21‑61 (MQ=255)

                                              catattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaagccga                                   >  1:2827410‑M2/21‑59 (MQ=255)

                                              catattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCa                        >  1:3104405‑M2/21‑70 (MQ=255)

                                                tattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGa                                                <  1:2651301‑M2/26‑1 (MQ=255)

                                                tattacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaagccga                                   <  1:2418172‑M2/39‑1 (MQ=255)

                                                 attacgtgggtaggatcACACATCTTTAGAGCCATCGt                                                     <  1:1961773‑M2/21‑1 (MQ=255)

                                                 attacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCtt                             >  1:1059769‑M2/18‑62 (MQ=255)

                                                  ttacgtgggtatgatcACACATCTTTAGAGCCATCGTCAGGa                                                >  1:4030595‑M2/17‑42 (MQ=255)

                                                  ttacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaagccgaa                                  >  1:2946407‑M2/17‑56 (MQ=255)

                                                  ttacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGtt                   >  1:1927216‑M2/17‑71 (MQ=255)

                                                  ttacgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGtt                   <  1:3512328‑M2/55‑1 (MQ=255)

                                                    acgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTg                  <  1:4447749‑M2/56‑1 (MQ=255)

                                                    acgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTg                  <  1:1680793‑M2/56‑1 (MQ=255)

                                                     cgtgggtaggatcACACATCTTTAGAGCCATCGTCAGGa                                                >  1:3822407‑M2/14‑39 (MQ=255)

                                                       tgggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAAc               >  1:4387589‑M2/12‑70 (MQ=255)

                                                        gggtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCa             >  1:261188‑M2/11‑71 (MQ=255)

                                                          gtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaa                                        >  1:4434363‑M2/9‑42 (MQ=255)

                                                          gtaggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCAtt           >  1:4737854‑M2/9‑71 (MQ=255)

                                                           taggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCAttt          <  1:1136182‑M2/64‑1 (MQ=255)

                                                           taggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCAttt          <  1:5172405‑M2/64‑1 (MQ=255)

                                                           taggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCAtt           >  1:4474007‑M2/8‑70 (MQ=255)

                                                            aggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTg                  >  1:858579‑M2/7‑62 (MQ=255)

                                                             ggatcACACATCTTTAGAGCCATCGTCAGGAGTGATgaa                                        >  1:2768280‑M2/6‑39 (MQ=255)

                                                             ggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGt                          >  1:1182952‑M2/6‑53 (MQ=255)

                                                             ggatcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCAtttt         >  1:3703447‑M2/6‑70 (MQ=255)

                                                                tcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGa     >  1:528854‑M2/3‑71 (MQ=255)

                                                                tcACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGa     >  1:3096876‑M2/3‑71 (MQ=255)

                                                                 cACACATCTTTAGAGCCATCGTCAGGAGTGATgaagcc                                     <  1:4879676‑M2/37‑1 (MQ=255)

                                                                  ACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATa   >  1:1079248‑M2/1‑71 (MQ=255)

                                                                   cacaTCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCt                              <  1:1083998/43‑1 (MQ=255)

                                                                   cacaTCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGa     >  1:5373341/1‑68 (MQ=255)

                                                                   cacaTCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATAc  <  1:3410245/71‑1 (MQ=255)

                                                                    acaTCTTTAGAGCCATCGTCAGGAGTGATgaagccgaagc                                >  1:2352201/1‑40 (MQ=255)

                                                                    acaTCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGt                          >  1:3522450/1‑46 (MQ=255)

                                                                    acaTCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATa   >  1:185413/1‑69 (MQ=255)

                                                                     caTCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTa        >  1:1049616/1‑63 (MQ=255)

                                                                      aTCTTTAGAGCCATCGTCAGGAGTGATgaagccga                                   <  1:2587836/35‑1 (MQ=255)

                                                                      aTCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACg      >  1:3890283/1‑64 (MQ=255)

AGGACACTTTCTGACCTTCGTCCAGAGATTTGTAACCATCGTTCTGGATAGCAGAGAAGTGTACGAACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATAC  >  AP009048/3920210‑3920347

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