Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,642,401	C→T	8.8%	T1082T (ACG→ACA)	yfhM ←	bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,642,401	0	C	T	8.8%	118.2 / 2.7	45	T1082T (ACG→ACA)	yfhM	bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (17/24);  new base T (2/2);  total (19/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.94e-01

CGTTTGTGCCGGGAACGCCGGACGGACGCCGATTTTCCACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTAAGATTAGTGATATCCAGCGTCAGACGCGAGGTATCGCCAC  >  CP009273/2642254‑2642549                                                                                                                                                    |                                                                                                                                                     cGTTTGTGCCGGGAACGCCGGACGGACGCCGATTTTCCACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCg                                                                                                                                                     <  2:110578/149‑1 (MQ=255)   tttGTGCCGGGAACGCCGGACGGATGCCGTTTTTCCACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTACCCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCgta                                                                                                                                                   <  2:167779/149‑1 (MQ=255)         ccgcaaaCGCAAGACGGACGCCGATTTTCCACTTCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATACACAGcaga                                                                                                                                                   >  1:332345/6‑140 (MQ=255)         ccGGGAACGCCGGACGGACGCCGATTTTCCACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGc                                                                                                                                             >  2:306907/1‑149 (MQ=255)         ccGGGAACGCCGGACGGACGCCGATTTTCCACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCAGGCCCCGGGATAAACAGCgca                                                                                                                                                   >  1:228432/1‑141 (MQ=255)         ccGGGAACGCCGGACGGACGCCGATTTTCCACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCGAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAAAGCGCGCACCGGGAAAAACAACgaa                                                                                                                                                   >  1:110748/1‑141 (MQ=255)               aCGCCGGACGGACGCCGATTTTCCACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGAGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCCCACCt                                                                                                                                       >  2:235984/1‑149 (MQ=255)                cGCCGGACGGACGCCGATTTTCCACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGca                                                                                                                                            >  1:273645/1‑143 (MQ=255)                   cggacggaCGCCGATTTTCCACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGgcg                                                                                                                                   <  2:542695/149‑1 (MQ=255)                                 ttttCCACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCt                                                                                                                     >  2:139898/1‑149 (MQ=255)                                      cACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCggg                                                                                                                <  2:422058/149‑1 (MQ=255)                                       aCTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGt                                                                                                               <  2:219931/149‑1 (MQ=255)                                         tGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGATCAGTAGAGTTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGa                                                                                                             <  2:463860/149‑1 (MQ=255)                                               tGCCGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCt                                                                                                       <  2:287056/149‑1 (MQ=255)                                                gCTGATCGGCCACGGTTCCACCCGGTAACGGTAACCCGCGAATGGTGGCCTGCATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGaa                                                                                                            <  1:512679/143‑1 (MQ=255)                                                  tGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGTGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGAc                                                                                                    >  2:126801/1‑149 (MQ=255)                                                  tGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGTGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGAc                                                                                                    >  2:126136/1‑149 (MQ=255)                                                       ggCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGGGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGAGAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCtta                                                                                                     <  1:179874/143‑3 (MQ=255)                                                         cAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTGCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCa                                                                                             <  2:256720/149‑1 (MQ=255)                                                          aaCGGTTTCGCCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTaaa                                                                                            <  2:635079/149‑1 (MQ=255)                                                              gTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCaa                                                                                        >  2:483380/1‑149 (MQ=255)                                                              gTTTCACCCGGTAACGCTAACCCGCTAATGGGGGCCAGAACTTCTCCACCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCaa                                                                                        <  2:119501/149‑1 (MQ=255)                                                                        gTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCg                                                                              <  2:339719/149‑1 (MQ=255)                                                                        gTAACGCTAACCCGCTAAGGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCg                                                                              <  2:344689/149‑1 (MQ=255)                                                                             gCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCCCCAGGAAAAAAACCGTAGCACGCACAGCCAGCGCTAAGTCAGCGGCTGGTACGGAATCGCGGACCAGTTCAAGCAAACCACCGGc                                                                               >  1:418767/1‑143 (MQ=255)                                                                                        aaTGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCaa                                                                    <  1:82859/143‑1 (MQ=255)                                                                                        aaTGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCa                                                              <  2:372575/149‑1 (MQ=255)                                                                                               gCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTCCGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAGCCGAACCACTAGCGACCAGGGCAACGTTCAGTTTTTg                                                       >  2:174788/1‑149 (MQ=255)                                                                                                  tGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCgg                                                    >  2:257111/1‑149 (MQ=255)                                                                                                    aaTTTCTCCATCGCCATACCCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGtt                                                  <  2:48453/149‑1 (MQ=255)                                                                                                       ttCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCACAGTTCAGTTTTTGCg                                                     >  1:447725/1‑143 (MQ=255)                                                                                                            cATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAAAGTTCGGTTTTTGCGGGTTa                                                >  1:170338/1‑143 (MQ=255)                                                                                                             aTCGCCATAACCCGGCAATGCTCGCACCAGGATAAACAGCGTAGTACACACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTGAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTaa                                         >  2:357494/1‑149 (MQ=255)                                                                                                              ccctcATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATc                                              <  1:517862/139‑1 (MQ=255)                                                                                                                   aTAACCCGGCAATGCTCGCACCGGGATAAACCGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCTATTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTAAGATTAg                                   <  2:427106/149‑1 (MQ=255)                                                                                                                   aTAACCCGGCAATGCTCGCACCGGGATAAACAGTGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTaa                                         <  1:113205/143‑1 (MQ=255)                                                                                                                   aTAACCCGGCAATGCTCGCACCGGGATAAACAGTGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTaa                                         <  1:113804/143‑1 (MQ=255)                                                                                                                   aTAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTaa                                         <  1:140383/143‑1 (MQ=255)                                                                                                                   aTAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTATGCGGATTATCGGTAAGATTAg                                   >  2:181659/1‑149 (MQ=255)                                                                                                                           gCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTAAGATTAGTGGTATcc                           >  2:510988/1‑149 (MQ=255)                                                                                                                            cAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATGGCTGACCAGTTCAAGCAAACCCCTGGCGGTCAGGGCACCGGTCAGTTTTTGCGGTTTATCGGTGAGGTTAGTGa                                >  1:452291/1‑143 (MQ=255)                                                                                                                               tGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTAAGATTAGTGatat                             <  1:529345/143‑1 (MQ=255)                                                                                                                                gCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTAAGATTAGTGATATc                            <  1:130671/143‑1 (MQ=255)                                                                                                                                         gggATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTAACGCTGCGCTGTAAGATTAGTGATATCCAGCGTCAGACGCGa             <  2:311128/149‑1 (MQ=255)                                                                                                                                             tAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTAAGATTAGTGATATCCAGCGTCAGAcgc               <  1:499065/143‑1 (MQ=255)                                                                                                                                                   gCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGGCTAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTAAGATTAGTGATATCCAGCGTCAGACGCGAGGTATCGccg   >  2:283147/1‑148 (MQ=255)                                                                                                                                                    cGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTAAGATTAGTGATATCCAGCGTCAGACGCGAGGTATCGCCAc  >  2:615158/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                     CGTTTGTGCCGGGAACGCCGGACGGACGCCGATTTTCCACTGCTTATGCTGATCGGCAACGGTTTCACCCGGTAACGCTAACCCGCTAATGGTGGCCTGAATTTCTCCATCGCCATAACCCGGCAATGCTCGCACCGGGATAAACAGCGTAGTACGCACACCTGGCGCTAATTCAACGGCTGCGGGTGAATCGCTGACCAGTTCAAGCAAACCACTGGCGGTCAGGGCAACGTTCAGTTTTTGCGGTTTATCGGTAAGATTAGTGATATCCAGCGTCAGACGCGAGGTATCGCCAC  >  CP009273/2642254‑2642549

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑