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%	294.1 / NA	61	intergenic (+182/‑22)	ssrA/intA	tmRNA/CP4‑57 prophage; integrase
Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (9/52); total (9/52)

TTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGT  >  NC_000913/2756088‑2756180

tttAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGc                                             >  1:563812/1‑50 (MQ=255)

 ttAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGc                                             <  1:5764506/49‑1 (MQ=255)

 ttAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGc                                             <  1:2627542/49‑1 (MQ=255)

  tAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGct                                            >  1:5837060/1‑48 (MQ=255)

  tAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGct                                            <  1:6847352/49‑2 (MQ=255)

  tAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGct                                            <  1:2461007/49‑2 (MQ=255)

  tAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGct                                            <  1:7657670/49‑2 (MQ=255)

   aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGcta                                           <  1:5666172/49‑3 (MQ=255)

     gCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAAc                                       <  1:1100790/50‑1 (MQ=255)

     gCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAAc                                       <  1:1157230/50‑1 (MQ=255)

      cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                      <  1:7632049/50‑1 (MQ=255)

      cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                      <  1:2699359/50‑1 (MQ=255)

       ccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGc                                     <  1:3707001/50‑1 (MQ=255)

         aTTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAg                                   <  1:7738214/50‑1 (MQ=255)

         aTTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAg                                   >  1:3291267/1‑50 (MQ=255)

          ttGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                  <  1:602068/50‑1 (MQ=255)

            gATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAggg                                 <  1:6472444/49‑1 (MQ=255)

             aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGgag                               <  1:818859/50‑1 (MQ=255)

             aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGga                                <  1:7578872/49‑1 (MQ=255)

             aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGga                                <  1:3891792/49‑1 (MQ=255)

             aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGga                                <  1:3898947/49‑1 (MQ=255)

              tAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGgaga                              <  1:1312831/50‑1 (MQ=255)

              tAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGgaga                              <  1:8194997/50‑1 (MQ=255)

                ggCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACt                            <  1:1470140/50‑1 (MQ=255)

                 gCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGCCTc                           <  1:2048510/50‑1 (MQ=255)

                  cccAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTcc                          <  1:4629908/50‑1 (MQ=255)

                    cAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTcccc                        <  1:2934362/50‑1 (MQ=255)

                    cAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTcccc                        <  1:6649109/50‑1 (MQ=255)

                    cAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTcccc                        <  1:7022613/50‑1 (MQ=255)

                       cGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcc                     >  1:7603324‑M1/1‑48 (MQ=255)

                       cGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcc                     <  1:6983719‑M1/50‑3 (MQ=255)

                        gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                    <  1:4166695‑M1/50‑4 (MQ=255)

                        gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                    >  1:6115511‑M1/1‑47 (MQ=255)

                        gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                    >  1:433862‑M1/1‑47 (MQ=255)

                        gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                    <  1:1634686‑M1/50‑4 (MQ=255)

                         aaaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctt                   <  1:632498‑M1/50‑5 (MQ=255)

                         aaaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctt                   <  1:2134830‑M1/50‑5 (MQ=255)

                          aaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                  <  1:8088846‑M1/50‑6 (MQ=255)

                          aaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                  <  1:7311603‑M1/50‑6 (MQ=255)

                          aaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                  <  1:984895‑M1/50‑6 (MQ=255)

                          aaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                  <  1:141186‑M1/50‑6 (MQ=255)

                            aGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttga                <  1:135773‑M1/50‑8 (MQ=255)

                            aGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttga                <  1:2573746‑M1/50‑8 (MQ=255)

                             gCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaa               <  1:8019138‑M1/50‑9 (MQ=255)

                             gCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaa               <  1:5931158‑M1/50‑9 (MQ=255)

                             gCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaa               <  1:6955941‑M1/50‑9 (MQ=255)

                             gCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaa               <  1:4041770‑M1/50‑9 (MQ=255)

                             gCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttga                >  1:1918153‑M1/1‑42 (MQ=255)

                              ctctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaa              <  1:4288086‑M1/50‑10 (MQ=255)

                                ctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa             >  1:1027785‑M1/1‑39 (MQ=255)

                                 tATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa             >  1:2261623‑M1/1‑38 (MQ=255)

                                   ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacagg         <  1:5277249‑M1/50‑15 (MQ=255)

                                   ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacagg         <  1:4762712‑M1/50‑15 (MQ=255)

                                   ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacagg         <  1:3357608‑M1/50‑15 (MQ=255)

                                   ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacag          <  1:3509024‑M1/49‑14 (MQ=255)

                                   ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacag          <  1:7358417‑M1/49‑14 (MQ=255)

                                   ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacag          >  1:3771193‑M1/1‑36 (MQ=255)

                                   ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacag          >  1:3911883‑M1/1‑36 (MQ=255)

                                   ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaaca           <  1:6082296‑M1/48‑13 (MQ=255)

                                   ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaaca           <  1:4897551‑M1/48‑13 (MQ=255)

                                     gTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacagga        <  1:2257016‑M1/49‑16 (MQ=255)

                                     gTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacagga        <  1:2200188‑M1/49‑16 (MQ=255)

                                      tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatg      <  1:1616375‑M1/50‑18 (MQ=255)

                                      tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggat       <  1:5762847‑M1/49‑17 (MQ=255)

                                        tACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgt     <  1:6180721‑M1/49‑19 (MQ=255)

                                         aCGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgta    <  1:459830‑M1/49‑20 (MQ=255)

                                         aCGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgta    <  1:1592730‑M1/49‑20 (MQ=255)

                                          cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc  <  1:2492498‑M1/50‑22 (MQ=255)

                                          cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc  <  1:6625171‑M1/50‑22 (MQ=255)

TTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGT  >  NC_000913/2756088‑2756180

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`