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%	396.3 / NA	79	intergenic (+182/‑22)	ssrA/intA	tmRNA/CP4‑57 prophage; integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (34/45);  total (34/45)

TTTAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTA  >  NC_000913/2756088‑2756182                                                  |                                              tttAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGc                                               >  1:960390/1‑50 (MQ=255)  ttAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGc                                               >  1:58504/1‑49 (MQ=255)  ttAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGc                                               >  1:1839566/1‑49 (MQ=255)   tAGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGct                                              <  1:1613993/49‑2 (MQ=255)    aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGcta                                             >  1:4553509/1‑47 (MQ=255)    aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGcta                                             >  1:2055563/1‑47 (MQ=255)    aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGcta                                             >  1:2009422/1‑47 (MQ=255)    aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGcta                                             >  1:2831421/1‑47 (MQ=255)    aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGcta                                             <  1:5338768/49‑3 (MQ=255)    aGGCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGGcta                                             >  1:1176916/1‑47 (MQ=255)      gCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAAc                                         <  1:1546516/50‑1 (MQ=255)      gCCCATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAAc                                         <  1:2822047/50‑1 (MQ=255)       cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                        <  1:1432950/50‑1 (MQ=255)       cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                        <  1:3376947/50‑1 (MQ=255)       cccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                        >  1:5268450/1‑50 (MQ=255)        ccATTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACg                                        >  1:4376254/1‑49 (MQ=255)          aTTGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAg                                     >  1:4056673/1‑50 (MQ=255)           ttGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                    >  1:6865474/1‑50 (MQ=255)           ttGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                    >  1:6253070/1‑50 (MQ=255)            tGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                    >  1:5921819/1‑49 (MQ=255)            tGATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                    >  1:4521397/1‑49 (MQ=255)             gATAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAgg                                    >  1:3092623/1‑48 (MQ=255)              aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGgag                                 <  1:5416431/50‑1 (MQ=255)              aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGgag                                 <  1:3579276/50‑1 (MQ=255)              aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGgag                                 <  1:6073812/50‑1 (MQ=255)              aTAGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGga                                  <  1:6973766/49‑1 (MQ=255)                aGGCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGAc                               >  1:1381254/1‑50 (MQ=255)                 ggCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGAc                               <  1:7124017/49‑1 (MQ=255)                 ggCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGAc                               <  1:6067797/49‑1 (MQ=255)                 ggCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACt                              <  1:933932/50‑1 (MQ=255)                 ggCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACt                              <  1:6702756/50‑1 (MQ=255)                  gCCCAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTc                             <  1:3816406/50‑1 (MQ=255)                   cccAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTcc                            <  1:2857700/50‑1 (MQ=255)                   cccAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTcc                            >  1:7539767/1‑50 (MQ=255)                   cccAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTcc                            >  1:3750531/1‑50 (MQ=255)                     cAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTccc                           >  1:1966341/1‑49 (MQ=255)                     cAACGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTccc                           >  1:266410/1‑49 (MQ=255)                      aaCGAAAAGCTTTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCA                         >  1:1066366‑M1/1‑50 (MQ=255)                      aaCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCA                         >  1:4292881‑M1/1‑50 (MQ=255)                      aaCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCA                         <  1:1904883‑M1/50‑1 (MQ=255)                       aCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAc                        <  1:3986146‑M1/50‑2 (MQ=255)                       aCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAc                        <  1:3451705‑M1/50‑2 (MQ=255)                       aCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAc                        >  1:3017336‑M1/1‑49 (MQ=255)                       aCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAc                        <  1:6825990‑M1/50‑2 (MQ=255)                       aCGAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAc                        <  1:5223679‑M1/50‑2 (MQ=255)                         gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                      <  1:5968692‑M1/50‑4 (MQ=255)                         gAAAAGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcct                      >  1:7145405‑M1/1‑47 (MQ=255)                          aaaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctt                     >  1:1421027‑M1/1‑46 (MQ=255)                          aaaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctt                     <  1:5277093‑M1/50‑5 (MQ=255)                          aaaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctt                     >  1:4935995‑M1/1‑46 (MQ=255)                          aaaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctt                     <  1:505506‑M1/50‑5 (MQ=255)                           aaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                    >  1:1067272‑M1/1‑45 (MQ=255)                           aaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                    <  1:1468073‑M1/50‑6 (MQ=255)                           aaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                    <  1:5133252‑M1/50‑6 (MQ=255)                           aaaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                    >  1:2723319‑M1/1‑45 (MQ=255)                            aaGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAccttt                    >  1:1756041‑M1/1‑44 (MQ=255)                             aGCTCTATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttg                   >  1:7002532‑M1/1‑43 (MQ=255)                               ctctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaa                <  1:3675692‑M1/50‑10 (MQ=255)                               ctctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaa                 >  1:5567814‑M1/1‑41 (MQ=255)                                tctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa               >  1:98553‑M1/1‑40 (MQ=255)                                tctATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa               >  1:1688201‑M1/1‑40 (MQ=255)                                  tATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa               <  1:5938489‑M1/48‑11 (MQ=255)                                  tATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa               <  1:7123474‑M1/48‑11 (MQ=255)                                  tATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa               >  1:6170742‑M1/1‑38 (MQ=255)                                  tATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa               <  1:4452235‑M1/48‑11 (MQ=255)                                  tATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa               <  1:1244417‑M1/48‑11 (MQ=255)                                  tATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa               <  1:6864132‑M1/48‑11 (MQ=255)                                  tATTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaa               <  1:234072‑M1/48‑11 (MQ=255)                                   aTTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacag            >  1:5900360‑M1/1‑37 (MQ=255)                                   aTTGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacag            >  1:3555351‑M1/1‑37 (MQ=255)                                    ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacag            <  1:492953‑M1/49‑14 (MQ=255)                                    ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacag            <  1:2848857‑M1/49‑14 (MQ=255)                                    ttGTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaac              <  1:4749716‑M1/47‑12 (MQ=255)                                      gTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggat         >  1:6647384‑M1/1‑34 (MQ=255)                                      gTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggat         >  1:5742688‑M1/1‑34 (MQ=255)                                      gTTTACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacagga          <  1:1078002‑M1/49‑16 (MQ=255)                                       tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatg        <  1:5359532‑M1/50‑18 (MQ=255)                                       tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatg        <  1:5481797‑M1/50‑18 (MQ=255)                                       tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatg        >  1:7119208‑M1/1‑33 (MQ=255)                                       tttACGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggat         <  1:1076162‑M1/49‑17 (MQ=255)                                          aCGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgta      <  1:910801‑M1/49‑20 (MQ=255)                                          aCGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgta      <  1:6314547‑M1/49‑20 (MQ=255)                                           cGTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtag     <  1:2157633‑M1/49‑21 (MQ=255)                                            gTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagcg   <  1:7347933‑M1/50‑23 (MQ=255)                                            gTTGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagcg   <  1:4037480‑M1/50‑23 (MQ=255)                                             ttGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagcga  <  1:7399539‑M1/50‑24 (MQ=255)                                             ttGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagcga  >  1:2700887‑M1/1‑27 (MQ=255)                                             ttGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagcga  <  1:3315953‑M1/50‑24 (MQ=255)                                             ttGGG‑CTAAACGCAGGGAGACTCCCCAcctttgaaaacaggatgtagcga  >  1:5032745‑M1/1‑27 (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: ‑