Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,635,059	C→T	S263S (TCG→TCA)	stfQ ←	Qin prophage, putative side tail fibre assembly protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,635,059	0	C	T	100.0%	141.3 / NA	52	S263S (TCG→TCA)	stfQ	Qin prophage, putative side tail fibre assembly protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (23/29);  total (23/29)

ACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTGCGCTTGCAGCAGTGCCGGACAGCGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATAACCATTAGGGAAAATGCTCGTGTTCGTG  >  NC_000913/1634955‑1635194                                                                                                         |                                                                                                                                        aCGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTcc                                                                                                       <  1:830973/139‑1 (MQ=1)  cGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTccc                                                                                                      <  2:1010781/139‑1 (MQ=11)    gTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTg                                                                                                    <  2:182248/139‑1 (MQ=11)              gtCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGt                                                                                          <  2:223609/139‑1 (MQ=14)              gtCCATGAGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGt                                                                                          >  1:688343/1‑139 (MQ=14)               tCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTc                                                                                         >  1:652235/1‑139 (MQ=14)                    gtgAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGcc                                                                                    >  2:438464/1‑139 (MQ=14)                    gtgAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGcc                                                                                    >  1:39145/1‑139 (MQ=14)                       aaCCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACt                                                                                 >  2:766918/1‑139 (MQ=17)                         ccAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCa                                                                                   >  2:531510/1‑135 (MQ=17)                         ccAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCa                                                                                   <  1:531510/135‑1 (MQ=17)                         ccAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTAc                                                                               >  1:801708/1‑139 (MQ=17)                         ccAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTAc                                                                               >  2:188345/1‑139 (MQ=17)                         ccAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTAc                                                                               >  1:338522/1‑139 (MQ=17)                            aTCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGc                                                                            <  2:801708/139‑1 (MQ=17)                            aTCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGc                                                                            >  2:506635/1‑139 (MQ=17)                                 aaCGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCttgtt                                                                       >  2:910760/1‑139 (MQ=18)                                  aCGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCttgttg                                                                      <  1:506635/139‑1 (MQ=18)                                        tGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTccc                                                                                                      >  2:24498/1‑101 (MQ=11)                                        tGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTccc                                                                                                      <  1:24498/101‑1 (MQ=11)                                              tGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATcc                                                          <  1:1119088/139‑1 (MQ=21)                                                aGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATcccc                                                        >  1:867853/1‑139 (MQ=21)                                                aGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATcccc                                                        <  1:96699/139‑1 (MQ=21)                                                aGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATcccc                                                        >  2:717717/1‑139 (MQ=21)                                                  cACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGt                                                                                          >  1:35134/1‑103 (MQ=14)                                                  cACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGt                                                                                          <  2:35134/103‑1 (MQ=14)                                                       aTACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTa                                                 >  1:756894/1‑139 (MQ=25)                                                             aCAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTg                                           >  2:936533/1‑139 (MQ=25)                                                             aCAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTg                                           >  1:785031/1‑139 (MQ=25)                                                                  atgcgcgtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATc                                      <  1:766918/126‑1 (MQ=37)                                                                  atgcgcgtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATc                                      <  2:688343/126‑1 (MQ=37)                                                                   tgcgcgtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg                                     <  1:717717/127‑1 (MQ=37)                                                                   tgcgcgtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg                                     <  2:652235/127‑1 (MQ=37)                                                                   tgcgcgtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg                                     <  2:148410/127‑1 (MQ=37)                                                                   tgcgcgtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg                                     <  1:34229/127‑1 (MQ=37)                                                                   tgcgcgtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg                                     <  2:756894/127‑1 (MQ=37)                                                                   tgcgcgtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg                                     <  1:908875/127‑1 (MQ=37)                                                                    gcgcgtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCt                                                   >  2:840780/12‑124 (MQ=25)                                                                    gcgcgtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCt                                                   <  1:840780/113‑1 (MQ=25)                                                                     cgcgtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcgcg                                   <  2:982483/129‑1 (MQ=255)                                                                         tgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCttgttg                                                                      <  2:198726/94‑1 (MQ=255)                                                                         tgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCttgttg                                                                      >  1:198726/7‑100 (MQ=255)                                                                         tgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGtat                               <  1:789683/133‑1 (MQ=255)                                                                         tgtgcaccTGCGCTTGCAGCAGAGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGtat                               <  2:148038/133‑1 (MQ=255)                                                                          gtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGtata                              <  1:188345/134‑1 (MQ=255)                                                                           tgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATaa                             >  1:529455/5‑139 (MQ=255)                                                                                    gcTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATAACCATTAggg                    >  2:209678/1‑139 (MQ=255)                                                                                     cTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCttgttg                                                                      >  2:162646/1‑88 (MQ=255)                                                                                     cTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCttgttg                                                                      <  1:162646/88‑1 (MQ=255)                                                                                     cTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATAACCATTAGGGa                   <  1:936533/139‑1 (MQ=255)                                                                                       tGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATAACCATTAGGGaaa                 <  1:370374/139‑1 (MQ=255)                                                                                                      cAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATAACCATTAGGGAAAATGCTCGTGTTCGTg  <  2:39145/139‑1 (MQ=255)                                                                                                         |                                                                                                                                        ACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTGCGCTTGCAGCAGTGCCGGACAGCGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATAACCATTAGGGAAAATGCTCGTGTTCGTG  >  NC_000913/1634955‑1635194

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑