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%	423.1 / NA	85	intergenic (+182/‑22)	ssrA/intA	tmRNA/CP4‑57 prophage; integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (37/48);  total (37/48)

TTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTA  >  NC_000913/2756088‑2756182                                                  |                                              tttAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGc                                               >  1:1125053/1‑50 (MQ=255)  ttAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGc                                               >  1:5700628/1‑49 (MQ=255)  ttAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGc                                               <  1:5462846/49‑1 (MQ=255)  ttAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGc                                               >  1:6143054/1‑49 (MQ=255)  ttAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGc                                               >  1:3739176/1‑49 (MQ=255)  ttAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGc                                               <  1:6929981/49‑1 (MQ=255)   tAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGct                                              >  1:1325775/1‑48 (MQ=255)   tAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGct                                              <  1:1806641/49‑2 (MQ=255)    aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGcta                                             >  1:3291471/1‑47 (MQ=255)    aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGcta                                             >  1:2637625/1‑47 (MQ=255)    aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGcta                                             <  1:4276602/49‑3 (MQ=255)      gCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAAc                                         <  1:1380504/50‑1 (MQ=255)      gCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAAc                                         <  1:2851199/50‑1 (MQ=255)      gCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAAc                                         <  1:5553215/50‑1 (MQ=255)      gCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAAc                                         <  1:6173987/50‑1 (MQ=255)      gCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAAc                                         <  1:6324498/50‑1 (MQ=255)       cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                        >  1:3175397/1‑50 (MQ=255)       cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                        >  1:1241037/1‑50 (MQ=255)       cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                        <  1:2537664/50‑1 (MQ=255)       cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                        <  1:4542043/50‑1 (MQ=255)       cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                        <  1:3453358/50‑1 (MQ=255)        ccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                        >  1:4440030/1‑49 (MQ=255)        ccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGc                                       <  1:8110450/50‑1 (MQ=255)        ccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGc                                       <  1:1704820/50‑1 (MQ=255)         cATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCa                                      <  1:400901/50‑1 (MQ=255)         cATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCa                                      <  1:5744944/50‑1 (MQ=255)         cATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCa                                      <  1:6136978/50‑1 (MQ=255)          aTTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAg                                     >  1:1449626/1‑50 (MQ=255)          aTTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAg                                     <  1:3380657/50‑1 (MQ=255)          aTTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAg                                     <  1:3893311/50‑1 (MQ=255)           ttGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                    <  1:311165/50‑1 (MQ=255)            tGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                    >  1:7098050/1‑49 (MQ=255)             gATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAggg                                   <  1:5889769/49‑1 (MQ=255)             gATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                    >  1:6623239/1‑48 (MQ=255)             gATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                    >  1:6924991/1‑48 (MQ=255)              aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                    >  1:8205237/1‑47 (MQ=255)               tAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGgaga                                >  1:5608524/1‑50 (MQ=255)                aGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGAc                               >  1:2099417/1‑50 (MQ=255)                 ggCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACt                              >  1:4452932/1‑50 (MQ=255)                  gCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTc                             >  1:329375/1‑50 (MQ=255)                  gCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTc                             >  1:4916710/1‑50 (MQ=255)                  gCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTc                             >  1:7588971/1‑50 (MQ=255)                   cccAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTcc                            >  1:5352022/1‑50 (MQ=255)                   cccAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTcc                            <  1:6491343/50‑1 (MQ=255)                       aCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAc                        <  1:7673815‑M1/50‑2 (MQ=255)                       aCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAc                        <  1:8187002‑M1/50‑2 (MQ=255)                        cGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcc                       >  1:4532813‑M1/1‑48 (MQ=255)                        cGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcc                       >  1:3766041‑M1/1‑48 (MQ=255)                         gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                      <  1:5671134‑M1/50‑4 (MQ=255)                         gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                      >  1:3300946‑M1/1‑47 (MQ=255)                         gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                      <  1:1972840‑M1/50‑4 (MQ=255)                          aaaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctt                     >  1:7509598‑M1/1‑46 (MQ=255)                           aaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                    >  1:3914495‑M1/1‑45 (MQ=255)                           aaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                    >  1:1771266‑M1/1‑45 (MQ=255)                            aaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                    >  1:13481‑M1/1‑44 (MQ=255)                             aGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttg                   >  1:307002‑M1/1‑43 (MQ=255)                              gCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttga                  >  1:7211128‑M1/1‑42 (MQ=255)                               ctctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaa                <  1:6912046‑M1/50‑10 (MQ=255)                               ctctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaa                <  1:3140751‑M1/50‑10 (MQ=255)                               ctctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaa                <  1:84415‑M1/50‑10 (MQ=255)                               ctctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaa                <  1:5277958‑M1/50‑10 (MQ=255)                               ctctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaa                <  1:2406689‑M1/50‑10 (MQ=255)                               ctctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaa                 >  1:1690987‑M1/1‑41 (MQ=255)                                tctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa               >  1:3140742‑M1/1‑40 (MQ=255)                                tctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa               >  1:8152866‑M1/1‑40 (MQ=255)                                  tATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa               >  1:4339094‑M1/1‑38 (MQ=255)                                  tATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa               <  1:3192371‑M1/48‑11 (MQ=255)                                      gTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggat         >  1:2211177‑M1/1‑34 (MQ=255)                                      gTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacagga          <  1:5343022‑M1/49‑16 (MQ=255)                                      gTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacagga          <  1:5335081‑M1/49‑16 (MQ=255)                                      gTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacagga          <  1:5010582‑M1/49‑16 (MQ=255)                                       tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatg        >  1:5582566‑M1/1‑33 (MQ=255)                                       tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatg        >  1:2396989‑M1/1‑33 (MQ=255)                                       tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatg        <  1:2865280‑M1/50‑18 (MQ=255)                                       tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatg        <  1:6426691‑M1/50‑18 (MQ=255)                                       tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggat         <  1:1310582‑M1/49‑17 (MQ=255)                                       tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggat         <  1:375294‑M1/49‑17 (MQ=255)                                       tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggat         <  1:3887051‑M1/49‑17 (MQ=255)                                         tACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgt       <  1:1082360‑M1/49‑19 (MQ=255)                                         tACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgt       <  1:4365937‑M1/49‑19 (MQ=255)                                         tACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgt       <  1:2110919‑M1/49‑19 (MQ=255)                                         tACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatg        >  1:3556278‑M1/1‑31 (MQ=255)                                          aCGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtag     >  1:2070939‑M1/1‑30 (MQ=255)                                          aCGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgta      <  1:6692833‑M1/49‑20 (MQ=255)                                          aCGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgta      <  1:6343109‑M1/49‑20 (MQ=255)                                           cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc    <  1:969339‑M1/50‑22 (MQ=255)                                           cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc    <  1:1637129‑M1/50‑22 (MQ=255)                                           cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc    >  1:1838251‑M1/1‑29 (MQ=255)                                           cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc    >  1:7701647‑M1/1‑29 (MQ=255)                                           cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc    <  1:293265‑M1/50‑22 (MQ=255)                                           cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc    <  1:6048401‑M1/50‑22 (MQ=255)                                           cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtag     <  1:2392658‑M1/49‑21 (MQ=255)                                            gTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagcg   <  1:7993729‑M1/50‑23 (MQ=255)                                            gTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagcg   <  1:1404043‑M1/50‑23 (MQ=255)                                            gTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc    >  1:7227043‑M1/1‑28 (MQ=255)                                             ttGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagcga  >  1:6663194‑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 < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑