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%	112.9 / NA	24	intergenic (+182/‑22)	ssrA/intA	tmRNA/CP4‑57 prophage; integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (11/13);  total (11/13)

TTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTT  >  NC_000913/2756088‑2756181                                                  |                                             tttAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGc                                              >  1:891235/1‑50 (MQ=255) tttAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGc                                              >  1:2275473/1‑50 (MQ=255)      gCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAAc                                        <  1:1854238/50‑1 (MQ=255)       cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                       <  1:1606888/50‑1 (MQ=255)        ccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                       >  1:1197981/1‑49 (MQ=255)           ttGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                   <  1:2101484/50‑1 (MQ=255)             gATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                   >  1:1135365/1‑48 (MQ=255)              aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                   >  1:503162/1‑47 (MQ=255)                 ggCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACt                             <  1:1939775/50‑1 (MQ=255)                  gCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTc                            <  1:738153/50‑1 (MQ=255)                     cAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTcccc                         <  1:1822695/50‑1 (MQ=255)                     cAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTccc                          >  1:1989929/1‑49 (MQ=255)                      aaCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCA                        <  1:1745788‑M1/50‑1 (MQ=255)                        cGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcc                      >  1:538304‑M1/1‑48 (MQ=255)                         gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                     <  1:2129800‑M1/50‑4 (MQ=255)                          aaaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctt                    >  1:754986‑M1/1‑46 (MQ=255)                           aaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                   <  1:1821415‑M1/50‑6 (MQ=255)                            aaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                   >  1:828661‑M1/1‑44 (MQ=255)                              gCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttga                 >  1:1877224‑M1/1‑42 (MQ=255)                               ctctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaa                >  1:1714579‑M1/1‑41 (MQ=255)                                   aTTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacag           >  1:845882‑M1/1‑37 (MQ=255)                                    ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacagg          <  1:1070461‑M1/50‑15 (MQ=255)                                           cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc   >  1:1281510‑M1/1‑29 (MQ=255)                                           cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtag    <  1:586313‑M1/49‑21 (MQ=255)                                            gTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagcg  <  1:1318174‑M1/50‑23 (MQ=255)                                            gTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggaggtagcg  <  1:89542‑M1/50‑23 (MQ=255)                                                  |                                             TTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTT  >  NC_000913/2756088‑2756181

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: ‑