BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,756,138	Δ1 bp	intergenic (+183/‑21)	ssrA → / → intA	tmRNA/CP4‑57 prophage; integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,756,137	0	C	.	100.0%	354.2 / NA	71	intergenic (+182/‑22)	ssrA/intA	tmRNA/CP4‑57 prophage; integrase
Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (40/31); total (40/31)

TTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGT  >  NC_000913/2756089‑2756180

ttAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGc                                             <  1:3239820/49‑1 (MQ=255)

 tAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGct                                            >  1:5024373/1‑48 (MQ=255)

 tAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGct                                            <  1:5933859/49‑2 (MQ=255)

    gCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAAc                                       <  1:3904967/50‑1 (MQ=255)

    gCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAAc                                       <  1:1974823/50‑1 (MQ=255)

     cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                      <  1:409216/50‑1 (MQ=255)

      ccATTGATAGGCCCAACGAAAAGCTCTATTGTTTGCGTTGGG‑CTAAACGc                                     <  1:4283119/50‑1 (MQ=255)

      ccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                      >  1:6270390/1‑49 (MQ=255)

       cATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGTG‑CTAAACg                                      >  1:5887098/1‑48 (MQ=255)

       cATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                      >  1:5245456/1‑48 (MQ=255)

       cATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCa                                    <  1:3998519/50‑1 (MQ=255)

        aTTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAg                                   >  1:1586938/1‑50 (MQ=255)

           gATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAggg                                 <  1:5085038/49‑1 (MQ=255)

           gATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAggg                                 <  1:167823/49‑1 (MQ=255)

           gATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                  >  1:4019295/1‑48 (MQ=255)

            aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                  >  1:4533853/1‑47 (MQ=255)

            aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                  >  1:5436882/1‑47 (MQ=255)

            aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                  >  1:547116/1‑47 (MQ=255)

            aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                  >  1:4279575/1‑47 (MQ=255)

             tAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGgaga                              <  1:4144925/50‑1 (MQ=255)

              aGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGAc                             >  1:648872/1‑50 (MQ=255)

               ggCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGAc                             <  1:1092866/49‑1 (MQ=255)

               ggCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACt                            <  1:3690857/50‑1 (MQ=255)

                gCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTc                           >  1:2384932/1‑50 (MQ=255)

                   cAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTcccc                        <  1:4296693/50‑1 (MQ=255)

                   cAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTcccc                        <  1:3180300/50‑1 (MQ=255)

                   cAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTccc                         >  1:140514/1‑49 (MQ=255)

                    aaCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCA                       >  1:4673460‑M1/1‑50 (MQ=255)

                    aaCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCA                       <  1:863705‑M1/50‑1 (MQ=255)

                    aaCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCA                       >  1:3864545‑M1/1‑50 (MQ=255)

                      cGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcc                     >  1:5120758‑M1/1‑48 (MQ=255)

                      cGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcc                     >  1:1787572‑M1/1‑48 (MQ=255)

                      cGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcc                     >  1:3417297‑M1/1‑48 (MQ=255)

                       gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                    >  1:4061322‑M1/1‑47 (MQ=255)

                       gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                    <  1:5299662‑M1/50‑4 (MQ=255)

                       gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                    <  1:285623‑M1/50‑4 (MQ=255)

                       gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                    <  1:4214527‑M1/50‑4 (MQ=255)

                        aaaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctt                   <  1:3617143‑M1/50‑5 (MQ=255)

                         aaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                  >  1:4801817‑M1/1‑45 (MQ=255)

                          aaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttg                 <  1:4475232‑M1/50‑7 (MQ=255)

                           aGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttga                <  1:4919984‑M1/50‑8 (MQ=255)

                           aGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttga                <  1:3687859‑M1/50‑8 (MQ=255)

                            gCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaa               <  1:5008456‑M1/50‑9 (MQ=255)

                             ctctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaa              <  1:1177978‑M1/50‑10 (MQ=255)

                             ctctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaa              <  1:2833325‑M1/50‑10 (MQ=255)

                             ctctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaa               >  1:34638‑M1/1‑41 (MQ=255)

                              tctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa             >  1:4593686‑M1/1‑40 (MQ=255)

                              tctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa             >  1:5174614‑M1/1‑40 (MQ=255)

                              tctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa             >  1:3609793‑M1/1‑40 (MQ=255)

                               ctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa             >  1:5491553‑M1/1‑39 (MQ=255)

                               ctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa             >  1:6310236‑M1/1‑39 (MQ=255)

                                tATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa             >  1:3881458‑M1/1‑38 (MQ=255)

                                tATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa             >  1:6154039‑M1/1‑38 (MQ=255)

                                 aTTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacag          >  1:1306580‑M1/1‑37 (MQ=255)

                                  ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacag          >  1:1263101‑M1/1‑36 (MQ=255)

                                  ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaaca           <  1:2281692‑M1/48‑13 (MQ=255)

                                   tGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacagga        >  1:6165006‑M1/1‑35 (MQ=255)

                                   tGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacagga        >  1:338767‑M1/1‑35 (MQ=255)

                                    gTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggat       >  1:439478‑M1/1‑34 (MQ=255)

                                    gTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacagga        <  1:6118619‑M1/49‑16 (MQ=255)

                                     tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatg      <  1:695905‑M1/50‑18 (MQ=255)

                                     tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatg      >  1:4399050‑M1/1‑33 (MQ=255)

                                     tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatg      <  1:4250708‑M1/50‑18 (MQ=255)

                                     tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggat       <  1:6048893‑M1/49‑17 (MQ=255)

                                     tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggat       <  1:3167233‑M1/49‑17 (MQ=255)

                                     tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggat       <  1:120221‑M1/49‑17 (MQ=255)

                                      ttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatg      >  1:1562769‑M1/1‑32 (MQ=255)

                                       tACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatg      >  1:5493328‑M1/1‑31 (MQ=255)

                                       tACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatg      >  1:4482620‑M1/1‑31 (MQ=255)

                                         cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc  <  1:159393‑M1/50‑22 (MQ=255)

                                         cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc  >  1:5006992‑M1/1‑29 (MQ=255)

                                         cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc  >  1:4774014‑M1/1‑29 (MQ=255)

                                          gTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc  >  1:1689396‑M1/1‑28 (MQ=255)

                                          gTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc  >  1:4144996‑M1/1‑28 (MQ=255)

TTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGT  >  NC_000913/2756089‑2756180

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 19 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`