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%	143.4 / NA	30	intergenic (+182/‑22)	ssrA/intA	tmRNA/CP4‑57 prophage; integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (5/25);  total (5/25)

TAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGT  >  NC_000913/2756090‑2756180                                                |                                            tAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGct                                            <  1:2194840/49‑2 (MQ=255)  aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGcta                                           <  1:1357710/49‑3 (MQ=255)  aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGcta                                           >  1:5359872/1‑47 (MQ=255)      ccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                      >  1:4896846/1‑49 (MQ=255)      ccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                      >  1:4494510/1‑49 (MQ=255)      ccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                      >  1:3863930/1‑49 (MQ=255)      ccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGc                                     <  1:3620842/50‑1 (MQ=255)       cATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                      >  1:3816618/1‑48 (MQ=255)       cATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCa                                    <  1:2998944/50‑1 (MQ=255)             tAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGgaga                              <  1:4913704/50‑1 (MQ=255)               ggCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACt                            <  1:2225266/50‑1 (MQ=255)                 cccAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTcc                          <  1:3927347/50‑1 (MQ=255)                  ccAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTccc                         <  1:3287423/50‑1 (MQ=255)                   cAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTcccc                        <  1:1962960/50‑1 (MQ=255)                    aaCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCA                       <  1:1275569‑M1/50‑1 (MQ=255)                     aCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAc                      <  1:2043793‑M1/50‑2 (MQ=255)                       gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                    <  1:463649‑M1/50‑4 (MQ=255)                         aaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                  <  1:1948158‑M1/50‑6 (MQ=255)                          aaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttg                 <  1:3144922‑M1/50‑7 (MQ=255)                           aGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttga                <  1:1912124‑M1/50‑8 (MQ=255)                            gCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaa               <  1:2843086‑M1/50‑9 (MQ=255)                            gCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaa               <  1:2138591‑M1/50‑9 (MQ=255)                                  ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacag          <  1:4146227‑M1/49‑14 (MQ=255)                                  ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacag          <  1:1633771‑M1/49‑14 (MQ=255)                                     tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggat       <  1:5302527‑M1/49‑17 (MQ=255)                                     tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggat       <  1:5586390‑M1/49‑17 (MQ=255)                                       tACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgt     <  1:320780‑M1/49‑19 (MQ=255)                                        aCGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgta    <  1:4194364‑M1/49‑20 (MQ=255)                                        aCGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgta    <  1:247029‑M1/49‑20 (MQ=255)                                        aCGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgta    <  1:1698181‑M1/49‑20 (MQ=255)                                        aCGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgta    <  1:1636020‑M1/49‑20 (MQ=255)                                         cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc  <  1:5351138‑M1/50‑22 (MQ=255)                                          gTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagc  >  1:5690871‑M1/1‑28 (MQ=255)                                                |                                            TAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGT  >  NC_000913/2756090‑2756180

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑