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%	119.7 / NA	25	intergenic (+182/‑22)	ssrA/intA	tmRNA/CP4‑57 prophage; integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (8/17);  total (8/17)

TAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTT  >  NC_000913/2756090‑2756181                                                |                                             tAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGct                                             >  1:1701073/1‑48 (MQ=255) tAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGct                                             >  1:188188/1‑48 (MQ=255)  aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGcta                                            >  1:2421043/1‑47 (MQ=255)  aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGcta                                            <  1:723652/49‑3 (MQ=255)  aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGcta                                            <  1:65241/49‑3 (MQ=255)  aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGcta                                            >  1:2579154/1‑47 (MQ=255)    gCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAAc                                        <  1:1827352/50‑1 (MQ=255)      ccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGc                                      <  1:4321479/50‑1 (MQ=255)       cATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCa                                     <  1:162468/50‑1 (MQ=255)        aTTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAg                                    >  1:4013616/1‑50 (MQ=255)          tGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                   >  1:1744451/1‑49 (MQ=255)            aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGga                                 <  1:1248079/49‑1 (MQ=255)              aGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGAc                              >  1:3660725/1‑50 (MQ=255)               ggCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGAc                              <  1:2654850/49‑1 (MQ=255)                gCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTc                            >  1:1732612/1‑50 (MQ=255)                    aaCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCA                        >  1:4277952‑M1/1‑50 (MQ=255)                       gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                     <  1:4077491‑M1/50‑4 (MQ=255)                        aaaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctt                    <  1:1612278‑M1/50‑5 (MQ=255)                        aaaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctt                    <  1:4226521‑M1/50‑5 (MQ=255)                         aaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                   >  1:2021520‑M1/1‑45 (MQ=255)                         aaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                   <  1:60669‑M1/50‑6 (MQ=255)                          aaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttg                  <  1:4130426‑M1/50‑7 (MQ=255)                          aaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttg                  <  1:1819327‑M1/50‑7 (MQ=255)                            gCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaa                <  1:3052927‑M1/50‑9 (MQ=255)                                tATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa              <  1:217015‑M1/48‑11 (MQ=255)                                 aTTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacag           >  1:2721077‑M1/1‑37 (MQ=255)                                  ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaaca            <  1:118849‑M1/48‑13 (MQ=255)                                        aCGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgta     <  1:2146285‑M1/49‑20 (MQ=255)                                        aCGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgta     <  1:1873760‑M1/49‑20 (MQ=255)                                         cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc   >  1:2141207‑M1/1‑29 (MQ=255)                                          gTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagcg  <  1:2788823‑M1/50‑23 (MQ=255)                                                |                                             TAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTT  >  NC_000913/2756090‑2756181

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑