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%	196.8 / NA	40	intergenic (+182/‑22)	ssrA/intA	tmRNA/CP4‑57 prophage; integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (21/19);  total (21/19)

TTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTT  >  NC_000913/2756088‑2756181                                                  |                                             tttAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGc                                              >  1:1899856/1‑50 (MQ=255) tttAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGc                                              >  1:317481/1‑50 (MQ=255)    aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGcta                                            >  1:1111465/1‑47 (MQ=255)    aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGcta                                            <  1:3351248/49‑3 (MQ=255)      gCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAAc                                        >  1:4221385/1‑50 (MQ=255)       cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                       <  1:1994216/50‑1 (MQ=255)       cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                       <  1:3178548/50‑1 (MQ=255)       cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                       >  1:741277/1‑50 (MQ=255)       cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                       >  1:1751281/1‑50 (MQ=255)        ccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                       >  1:1045134/1‑49 (MQ=255)         cATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                       >  1:369323/1‑48 (MQ=255)          aTTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAg                                    >  1:1538630/1‑50 (MQ=255)          aTTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAg                                    <  1:3028160/50‑1 (MQ=255)           ttGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                   >  1:2662283/1‑50 (MQ=255)            tGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                   >  1:4242227/1‑49 (MQ=255)               tAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGgaga                               >  1:3283054/1‑50 (MQ=255)               tAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGgaga                               <  1:2144893/50‑1 (MQ=255)               tAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGgaga                               <  1:1784118/50‑1 (MQ=255)                 ggCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACt                             >  1:66469/1‑50 (MQ=255)                 ggCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACt                             >  1:928733/1‑50 (MQ=255)                    ccAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTccc                          >  1:95728/1‑50 (MQ=255)                     cAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTcccc                         <  1:3467474/50‑1 (MQ=255)                       aCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAc                       <  1:2666202‑M1/50‑2 (MQ=255)                         gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                     <  1:702231‑M1/50‑4 (MQ=255)                         gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                     <  1:3081776‑M1/50‑4 (MQ=255)                          aaaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctt                    >  1:2242664‑M1/1‑46 (MQ=255)                          aaaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctt                    <  1:2024242‑M1/50‑5 (MQ=255)                            aaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttg                  <  1:1052270‑M1/50‑7 (MQ=255)                            aaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                   >  1:113230‑M1/1‑44 (MQ=255)                             aGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttga                 <  1:1680451‑M1/50‑8 (MQ=255)                             aGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttga                 <  1:1513517‑M1/50‑8 (MQ=255)                              gCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttga                 >  1:307758‑M1/1‑42 (MQ=255)                               ctctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaa               <  1:936244‑M1/50‑10 (MQ=255)                               ctctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaa                >  1:2598929‑M1/1‑41 (MQ=255)                                    ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaac             <  1:3490938‑M1/47‑12 (MQ=255)                                      gTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggat        >  1:2066408‑M1/1‑34 (MQ=255)                                      gTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacagga         <  1:4111913‑M1/49‑16 (MQ=255)                                       tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatg       >  1:3444851‑M1/1‑33 (MQ=255)                                          aCGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgta     <  1:4296978‑M1/49‑20 (MQ=255)                                           cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc   <  1:4163830‑M1/50‑22 (MQ=255)                                           cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc   >  1:1438762‑M1/1‑29 (MQ=255)                                            gTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagcg  <  1:3737075‑M1/50‑23 (MQ=255)                                            gTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc   >  1:1701731‑M1/1‑28 (MQ=255)                                            gTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc   >  1:1045206‑M1/1‑28 (MQ=255)                                                  |                                             TTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTT  >  NC_000913/2756088‑2756181

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑