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%	130.5 / NA	28	intergenic (+182/‑22)	ssrA/intA	tmRNA/CP4‑57 prophage; integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (12/16);  total (12/16)

TTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTA  >  NC_000913/2756088‑2756182                                                  |                                              tttAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGc                                               >  1:1526109/1‑50 (MQ=255)   tAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGct                                              >  1:980301/1‑48 (MQ=255)      gCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAAc                                         <  1:1557000/50‑1 (MQ=255)      gCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAAc                                         <  1:1976643/50‑1 (MQ=255)          aTTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAg                                     >  1:295776/1‑50 (MQ=255)             gATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAggg                                   <  1:897946/49‑1 (MQ=255)             gATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAggg                                   <  1:853169/49‑1 (MQ=255)              aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGgag                                 <  1:2327973/50‑1 (MQ=255)              aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGga                                  <  1:649071/49‑1 (MQ=255)               tAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGgaga                                >  1:703271/1‑50 (MQ=255)                  gCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTc                             <  1:1780513/50‑1 (MQ=255)                  gCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTc                             <  1:387157/50‑1 (MQ=255)                   cccAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTcc                            >  1:1809005/1‑50 (MQ=255)                     cAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTcccc                          <  1:325869/50‑1 (MQ=255)                        cGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcc                       >  1:1371512‑M1/1‑48 (MQ=255)                         gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                      <  1:2596216‑M1/50‑4 (MQ=255)                         gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                      >  1:1451536‑M1/1‑47 (MQ=255)                           aaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                    >  1:698746‑M1/1‑45 (MQ=255)                             aGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttg                   >  1:20969‑M1/1‑43 (MQ=255)                             aGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttg                   >  1:1770379‑M1/1‑43 (MQ=255)                              gCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttga                  >  1:2340318‑M1/1‑42 (MQ=255)                               ctctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaa                <  1:100354‑M1/50‑10 (MQ=255)                               ctctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaa                <  1:2088336‑M1/50‑10 (MQ=255)                                tctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa               >  1:84417‑M1/1‑40 (MQ=255)                                      gTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggat         >  1:279677‑M1/1‑34 (MQ=255)                                         tACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgt       <  1:571409‑M1/49‑19 (MQ=255)                                         tACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgt       <  1:1025765‑M1/49‑19 (MQ=255)                                           cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtag     <  1:386882‑M1/49‑21 (MQ=255)                                             ttGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagcga  >  1:2478414‑M1/1‑27 (MQ=255)                                             ttGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagcga  <  1:873688‑M1/50‑24 (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: ‑