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%	225.2 / NA	46	intergenic (+182/‑22)	ssrA/intA	tmRNA/CP4‑57 prophage; integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (18/28);  total (18/28)

AGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGT  >  NC_000913/2756091‑2756180                                               |                                            aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGct                                            <  1:2339369/48‑2 (MQ=255) aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGct                                            <  1:1611422/48‑2 (MQ=255)    cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAAc                                       <  1:637376/49‑1 (MQ=255)    cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAAc                                       <  1:528723/49‑1 (MQ=255)    cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAAc                                       <  1:477844/49‑1 (MQ=255)     ccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                      >  1:1052852/1‑49 (MQ=255)     ccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                      >  1:979464/1‑49 (MQ=255)        ttGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAg                                   <  1:2344840/49‑1 (MQ=255)          gATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                  <  1:2107199/48‑1 (MQ=255)          gATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                  >  1:822304/1‑48 (MQ=255)           aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAggg                                 <  1:507297/48‑1 (MQ=255)           aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGga                                <  1:569344/49‑1 (MQ=255)            tAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGgag                               <  1:1524617/49‑1 (MQ=255)            tAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGgag                               <  1:1788666/49‑1 (MQ=255)              ggCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGgaga                              <  1:832140/48‑1 (MQ=255)               gCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACt                            >  1:1078927/1‑49 (MQ=255)                cccAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTc                           >  1:1045065/1‑49 (MQ=255)                cccAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTc                           <  1:1974176/49‑1 (MQ=255)                 ccAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTcc                          >  1:1352673/1‑49 (MQ=255)                  cAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTccc                         <  1:1727060/49‑1 (MQ=255)                   aaCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTcccc                        <  1:2133435/49‑1 (MQ=255)                   aaCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTccc                         >  1:1503448/1‑48 (MQ=255)                    aCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCA                       <  1:2285541‑M1/49‑1 (MQ=255)                     cGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAc                      <  1:1704386‑M1/49‑2 (MQ=255)                     cGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAc                      <  1:1625808‑M1/49‑2 (MQ=255)                      gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcc                     >  1:1053013‑M1/1‑47 (MQ=255)                      gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcc                     >  1:1506913‑M1/1‑47 (MQ=255)                         aaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                  <  1:1320527‑M1/49‑6 (MQ=255)                         aaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                  >  1:375263‑M1/1‑44 (MQ=255)                            ctctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaa               <  1:413930‑M1/49‑9 (MQ=255)                             tctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaa               >  1:2119345‑M1/1‑40 (MQ=255)                              ctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa             >  1:2214765‑M1/1‑39 (MQ=255)                                aTTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa             >  1:1197415‑M1/1‑37 (MQ=255)                                 ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacag          <  1:191879‑M1/49‑14 (MQ=255)                                 ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaaca           <  1:2191080‑M1/48‑13 (MQ=255)                                 ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaaca           <  1:610824‑M1/48‑13 (MQ=255)                                 ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaaca           <  1:743575‑M1/48‑13 (MQ=255)                                 ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaaca           <  1:1336848‑M1/48‑13 (MQ=255)                                 ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa             <  1:1501462‑M1/46‑11 (MQ=255)                                   gTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacagga        >  1:2186134‑M1/1‑34 (MQ=255)                                    tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacagga        <  1:315404‑M1/48‑16 (MQ=255)                                     ttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatg      >  1:158323‑M1/1‑32 (MQ=255)                                       aCGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatg      >  1:1636166‑M1/1‑30 (MQ=255)                                        cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtag   <  1:423084‑M1/49‑21 (MQ=255)                                        cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgta    <  1:1907416‑M1/48‑20 (MQ=255)                                         gTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc  <  1:420023‑M1/49‑22 (MQ=255)                                         gTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc  >  1:791783‑M1/1‑28 (MQ=255)                                         gTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgaagc  >  1:807810‑M1/1‑28 (MQ=255)                                               |                                            AGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGT  >  NC_000913/2756091‑2756180

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑