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%	224.4 / NA	46	intergenic (+182/‑22)	ssrA/intA	tmRNA/CP4‑57 prophage; integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (22/24);  total (22/24)

TAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGT  >  NC_000913/2756090‑2756180                                                |                                            tAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGct                                            <  1:1342396/49‑2 (MQ=255)  aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGcta                                           <  1:646249/49‑3 (MQ=255)     cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                      >  1:1959788/1‑50 (MQ=255)     cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                      <  1:1122967/50‑1 (MQ=255)      ccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                      >  1:2352537/1‑49 (MQ=255)      ccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGc                                     <  1:128303/50‑1 (MQ=255)       cATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                      >  1:2564556/1‑48 (MQ=255)       cATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                      >  1:1407555/1‑48 (MQ=255)        aTTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAg                                   >  1:104862/1‑50 (MQ=255)           gATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                  >  1:1667671/1‑48 (MQ=255)            aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGgag                               <  1:776049/50‑1 (MQ=255)            aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGga                                <  1:1053555/49‑1 (MQ=255)            aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGga                                <  1:1822492/49‑1 (MQ=255)              aGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGAc                             >  1:2447255/1‑50 (MQ=255)               ggCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACt                            <  1:865808/50‑1 (MQ=255)                gCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTc                           >  1:2721519/1‑50 (MQ=255)                  ccAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTccc                         <  1:1328913/50‑1 (MQ=255)                  ccAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTccc                         >  1:2051163/1‑50 (MQ=255)                   cAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTccc                         >  1:2296720/1‑49 (MQ=255)                    aaCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCA                       >  1:365344‑M1/1‑50 (MQ=255)                     aCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAc                      <  1:1067533‑M1/50‑2 (MQ=255)                         aaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                  >  1:1888570‑M1/1‑45 (MQ=255)                          aaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                  >  1:838230‑M1/1‑44 (MQ=255)                           aGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttga                <  1:1045528‑M1/50‑8 (MQ=255)                           aGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttga                <  1:59028‑M1/50‑8 (MQ=255)                            gCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaa               <  1:2117219‑M1/50‑9 (MQ=255)                               ctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa             >  1:1079703‑M1/1‑39 (MQ=255)                                tATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa             >  1:1203462‑M1/1‑38 (MQ=255)                                tATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa             >  1:1004182‑M1/1‑38 (MQ=255)                                  ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacagg         <  1:1434435‑M1/50‑15 (MQ=255)                                  ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacag          <  1:1063573‑M1/49‑14 (MQ=255)                                  ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaaca           <  1:2068680‑M1/48‑13 (MQ=255)                                  ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaac            <  1:2661998‑M1/47‑12 (MQ=255)                                  ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaac            <  1:2791187‑M1/47‑12 (MQ=255)                                   tGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacagga        >  1:1618‑M1/1‑35 (MQ=255)                                    gTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacagga        <  1:2399133‑M1/49‑16 (MQ=255)                                     tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatg      >  1:511568‑M1/1‑33 (MQ=255)                                       tACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatg      >  1:57813‑M1/1‑31 (MQ=255)                                        aCGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtag   >  1:340629‑M1/1‑30 (MQ=255)                                        aCGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgta    <  1:1599862‑M1/49‑20 (MQ=255)                                        aCGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgta    <  1:1101866‑M1/49‑20 (MQ=255)                                        aCGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgta    <  1:971321‑M1/49‑20 (MQ=255)                                         cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc  <  1:333407‑M1/50‑22 (MQ=255)                                         cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc  <  1:2019058‑M1/50‑22 (MQ=255)                                         cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc  >  1:1432436‑M1/1‑29 (MQ=255)                                         cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtag   <  1:2128546‑M1/49‑21 (MQ=255)                                         cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtag   <  1:531951‑M1/49‑21 (MQ=255)                                          gTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc  >  1:460722‑M1/1‑28 (MQ=255)                                                |                                            TAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGT  >  NC_000913/2756090‑2756180

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑