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%	154.6 / NA	32	intergenic (+182/‑22)	ssrA/intA	tmRNA/CP4‑57 prophage; integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (9/23);  total (9/23)

TTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTA  >  NC_000913/2756089‑2756182                                                 |                                              ttAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGc                                               <  1:1249554/49‑1 (MQ=255)  tAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGct                                              <  1:2064447/49‑2 (MQ=255)     gCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAAc                                         >  1:906407/1‑50 (MQ=255)      cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                        >  1:792515/1‑50 (MQ=255)         aTTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAg                                     >  1:1197338/1‑50 (MQ=255)          ttGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                    <  1:1247134/50‑1 (MQ=255)            gATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAggg                                   <  1:1396465/49‑1 (MQ=255)             aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGga                                  <  1:1039608/49‑1 (MQ=255)             aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGga                                  <  1:645654/49‑1 (MQ=255)               aGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGAc                               >  1:946992/1‑50 (MQ=255)                 gCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTc                             <  1:110805/50‑1 (MQ=255)                      aCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAc                        <  1:911998‑M1/50‑2 (MQ=255)                      aCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAc                        <  1:359899‑M1/50‑2 (MQ=255)                        gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                      <  1:1423404‑M1/50‑4 (MQ=255)                        gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                      <  1:456434‑M1/50‑4 (MQ=255)                         aaaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctt                     <  1:798344‑M1/50‑5 (MQ=255)                         aaaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctt                     <  1:2240952‑M1/50‑5 (MQ=255)                            aGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttga                  <  1:1047064‑M1/50‑8 (MQ=255)                            aGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttg                   >  1:2052920‑M1/1‑43 (MQ=255)                              ctctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaa                <  1:883726‑M1/50‑10 (MQ=255)                              ctctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaa                 >  1:570132‑M1/1‑41 (MQ=255)                                 tATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa               >  1:2146664‑M1/1‑38 (MQ=255)                                 tATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa               <  1:16049‑M1/48‑11 (MQ=255)                                 tATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa               >  1:131379‑M1/1‑38 (MQ=255)                                   ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacagg           <  1:1263573‑M1/50‑15 (MQ=255)                                   ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaac              <  1:768465‑M1/47‑12 (MQ=255)                                     gTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacagga          <  1:811061‑M1/49‑16 (MQ=255)                                      tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggat         <  1:2112799‑M1/49‑17 (MQ=255)                                         aCGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgta      <  1:857999‑M1/49‑20 (MQ=255)                                          cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc    <  1:2123258‑M1/50‑22 (MQ=255)                                          cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc    >  1:1421844‑M1/1‑29 (MQ=255)                                          cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtag     <  1:537337‑M1/49‑21 (MQ=255)                                           gTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagcg   <  1:1194014‑M1/50‑23 (MQ=255)                                            ttGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagcga  <  1:1750534‑M1/50‑24 (MQ=255)                                                 |                                              TTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTA  >  NC_000913/2756089‑2756182

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑