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%	347.1 / NA	69	intergenic (+182/‑22)	ssrA/intA	tmRNA/CP4‑57 prophage; integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (29/40);  total (29/40)

TTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTA  >  NC_000913/2756088‑2756182                                                  |                                              tttAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGc                                               >  1:2105142/1‑50 (MQ=255)  ttAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGc                                               <  1:2415971/49‑1 (MQ=255)   tAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGct                                              <  1:465965/49‑2 (MQ=255)    aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGcta                                             >  1:895166/1‑47 (MQ=255)    aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGcta                                             >  1:4370934/1‑47 (MQ=255)    aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGcta                                             <  1:6538036/49‑3 (MQ=255)      gCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAAc                                         <  1:4958180/50‑1 (MQ=255)      gCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAAc                                         >  1:2478191/1‑50 (MQ=255)       cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                        >  1:476346/1‑50 (MQ=255)       cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                        >  1:5948615/1‑50 (MQ=255)       cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                        <  1:2173809/50‑1 (MQ=255)       cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                        <  1:3659109/50‑1 (MQ=255)        ccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGc                                       <  1:3062935/50‑1 (MQ=255)         cATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                        >  1:1683431/1‑48 (MQ=255)         cATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                        >  1:4528335/1‑48 (MQ=255)         cATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCa                                      <  1:3404293/50‑1 (MQ=255)          aTTGATAGGCCTAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAg                                     <  1:729224/50‑1 (MQ=255)          aTTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAg                                     <  1:5719492/50‑1 (MQ=255)          aTTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAg                                     >  1:1130870/1‑50 (MQ=255)           ttGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                    <  1:3586185/50‑1 (MQ=255)           ttGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                    <  1:3504889/50‑1 (MQ=255)             gATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAggg                                   <  1:4288233/49‑1 (MQ=255)             gATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                    >  1:3564412/1‑48 (MQ=255)              aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                    >  1:4394182/1‑47 (MQ=255)              aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                    >  1:6221639/1‑47 (MQ=255)               tAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGgaga                                >  1:5348886/1‑50 (MQ=255)               tAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGgaga                                <  1:4106411/50‑1 (MQ=255)               tAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGgaga                                >  1:2682572/1‑50 (MQ=255)                 ggCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGAc                               <  1:5662459/49‑1 (MQ=255)                 ggCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACt                              >  1:5801798/1‑50 (MQ=255)                 ggCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACt                              <  1:1513677/50‑1 (MQ=255)                 ggCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACt                              <  1:2255705/50‑1 (MQ=255)                  gCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTc                             <  1:5712463/50‑1 (MQ=255)                  gCCCAACGAAAAGCTCTAATGTTTACGTTGGG‑CTAAACGCAGGGAGACTc                             >  1:3981922/1‑50 (MQ=255)                   cccAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTcc                            >  1:3158041/1‑50 (MQ=255)                    ccAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTccc                           >  1:529162/1‑50 (MQ=255)                      aaCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCA                         >  1:4764008‑M1/1‑50 (MQ=255)                       aCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAc                        >  1:1599564‑M1/1‑49 (MQ=255)                       aCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAc                        <  1:5574046‑M1/50‑2 (MQ=255)                       aCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAc                        <  1:3480313‑M1/50‑2 (MQ=255)                        cGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcc                       >  1:2021655‑M1/1‑48 (MQ=255)                        cGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcc                       <  1:1966225‑M1/50‑3 (MQ=255)                         gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                      <  1:2099649‑M1/50‑4 (MQ=255)                         gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                      >  1:1067846‑M1/1‑47 (MQ=255)                         gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                      >  1:5912118‑M1/1‑47 (MQ=255)                         gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                      >  1:6095026‑M1/1‑47 (MQ=255)                         gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                      >  1:1295957‑M1/1‑47 (MQ=255)                          aaaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctt                     >  1:6382872‑M1/1‑46 (MQ=255)                           aaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                    <  1:557874‑M1/50‑6 (MQ=255)                           aaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                    <  1:5102352‑M1/50‑6 (MQ=255)                            aaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttg                   <  1:4266533‑M1/50‑7 (MQ=255)                            aaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttg                   <  1:1421573‑M1/50‑7 (MQ=255)                            aaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                    >  1:509624‑M1/1‑44 (MQ=255)                             aGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttga                  <  1:612848‑M1/50‑8 (MQ=255)                              gCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaa                 <  1:4719729‑M1/50‑9 (MQ=255)                                tctATTGTTTACGTTGGG‑CTAAACGCAGGGCGACTCCCCAcctttgaaaa               >  1:885995‑M1/1‑40 (MQ=255)                                  tATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa               >  1:4424967‑M1/1‑38 (MQ=255)                                    ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacag            <  1:1391618‑M1/49‑14 (MQ=255)                                    ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacag            <  1:276618‑M1/49‑14 (MQ=255)                                    ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaaca             <  1:994774‑M1/48‑13 (MQ=255)                                    ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaaca             <  1:3751046‑M1/48‑13 (MQ=255)                                    ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaac              <  1:262891‑M1/47‑12 (MQ=255)                                      gTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacagga          <  1:4112579‑M1/49‑16 (MQ=255)                                      gTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacagga          <  1:5817128‑M1/49‑16 (MQ=255)                                       tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatg        <  1:3132910‑M1/50‑18 (MQ=255)                                       tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggat         <  1:5754457‑M1/49‑17 (MQ=255)                                         tACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgt       <  1:3203791‑M1/49‑19 (MQ=255)                                         tACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatg        >  1:4690004‑M1/1‑31 (MQ=255)                                          aCGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtag     >  1:3082369‑M1/1‑30 (MQ=255)                                          aCGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgta      <  1:4891055‑M1/49‑20 (MQ=255)                                           cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc    <  1:5994190‑M1/50‑22 (MQ=255)                                           cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc    <  1:4781231‑M1/50‑22 (MQ=255)                                           cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtag     <  1:870625‑M1/49‑21 (MQ=255)                                           cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtag     <  1:4634073‑M1/49‑21 (MQ=255)                                             ttGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagcga  >  1:4100402‑M1/1‑27 (MQ=255)                                                  |                                              TTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTA  >  NC_000913/2756088‑2756182

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑