Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,968,935	A→C	30.4%	D340A (GAT→GCT)	PP_3498 →	transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,968,935	0	A	C	30.4%	21.7 / 14.3	23	D340A (GAT→GCT)	PP_3498	transposase
Reads supporting (aligned to +/- strand):  ref base A (7/9);  new base C (2/5);  total (9/14)
Fisher's exact test for biased strand distribution p-value = 6.57e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.63e-01

ATTGGGCAAGATGAGCAAGCGCGGTGACGGCTACATACGCAGCCTGATGATCCAGGGCGCGCATTCCGTCTTGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGATGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAATCGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGATCAGGTTTACCAACGCAAACCGAACGAAA  >  NC_002947/3968831‑3969069                                                                                                         |                                                                                                                                       gtcagaggctcatagccgcctccggtttttcgttcggtttgcgttggtaaacctgatcgctctgtaacagggcccagataatccgcagatttcgattagccagcCTGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAagga                                                                                           <  1:448021‑M2/46‑1 (MQ=255)    agaggctcatagccgcttccggtttttcgttcggtttgcgttggtaaacctgatcgctctgtaacagggcccagataatccgcagatttcgattagccagcCTGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAggc                                                                                        <  2:128313‑M2/49‑1 (MQ=255)    agaggctcatagccgcctccggtttttcgttcggtttgcgttggtaaacctgatcgctctgtaacagggcccatataatccgcagatttcgattagccagcCTGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAggc                                                                                        <  2:546505‑M2/49‑1 (MQ=255)                            ttttcgttcggtttgcgttggtaaacctgatcgctctgtaacagggcccagataatccgcagatttcgattagccagATGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAagga                                                                                           <  2:601899‑M2/46‑1 (MQ=255)                            ttttcgttcggtttgcgttggtaaacctgatcgctctgtaacagggcccagataatccgcagatttcgattagccagATGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAagga                                                                                           >  1:601899‑M2/78‑123 (MQ=255)                                            ttggtaaacctgatcgctctgtaacagggcccagataatccgcagatttcgattagccagcCTGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAggc                                                                                        >  2:48391‑M2/62‑110 (MQ=255)                                            ttggtaaacctgatcgctctgtaacagggcccagataatccgcagatttcgattagccagcCTGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAggc                                                                                        <  1:48391‑M2/49‑1 (MQ=255)                                                      ctgatcgctctgtaacagggcccagataatccgcagatttcgattagccagATGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAATCGAAATCTGCg                                                          >  2:511204‑M2/52‑130 (MQ=255)                                                      ctgatcgctctgtaacagggcccagataatccgcagatttcgattagccagATGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAATCGAAATCTGCg                                                          <  1:511204‑M2/79‑1 (MQ=255)                                                          cgcgcATTCCGTCTTGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGATGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAATCGAAATCTGCGGATTATATGGGCCCTGTTACagag                                  <  1:236450/150‑1 (MQ=32)                                                           gcgcATTCCGTCTTGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGATGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAATCGAAATCTGCGGATTATATGGGCCCTGTTACAGAGc                                 >  1:159148/1‑150 (MQ=32)                                                                       ttGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGATGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAATCGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGATCAGGTTTAc                     <  2:19253/150‑1 (MQ=32)                                                                           gCCAGCTAAGGCCTGATTCCGATCAGCCAGATGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAATCGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGATCAGGTTTACCAAc                 <  2:546777/150‑1 (MQ=32)                                                                               gCTAAGGCCTGATTGCGATCAGCCAGATGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAATCGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGGTCAGGTTTACCAACGCaa             >  2:37138/1‑150 (MQ=17)                                                                                     gCCTGATTCCGATCAGCCAGATGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAATCGAAATCTGCGGATTATATGGGCCCTGt                                         <  2:334808/116‑1 (MQ=33)                                                                                     gCCTGATTCCGATCAGCCAGATGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAATCGAAATCTGCGGATTATATGGGCCCTGt                                         >  1:334808/1‑116 (MQ=33)                                                                                      ccTGATTCCGATCAGCCAGATGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAATCGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGATCAGGTTTACCAACGCAAACcgaac      <  2:159148/150‑1 (MQ=32)                                                                                      ccTGATTCCGATCAGCCAGATGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAATCGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGATCAGGTTTACCAACGCAAACcgaac      >  1:421152/1‑150 (MQ=32)                                                                                          aTTCCGATCAGCCAGATGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAATCGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGATCAGGTTTACCAACGCAAACCGAACGaaa  <  2:501063/150‑1 (MQ=32)                                                                                              gattagccagcCTGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAATCGAAATCTGCGGATTATATGGGc                                              <  2:283205‑M2/91‑1 (MQ=255)                                                                                              gattagccagcCTGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAATCGAAATCTGCGGATTATATGGGc                                              >  1:283205‑M2/12‑102 (MQ=255)                                                                                                        gATGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAATCGAAATCTGc                                                           <  1:425021‑M2/78‑1 (MQ=255)                                                                                                        gATGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAATCGAAATCTGc                                                           >  2:425021‑M2/2‑79 (MQ=255)                                                                                                         |                                                                                                                                       ATTGGGCAAGATGAGCAAGCGCGGTGACGGCTACATACGCAGCCTGATGATCCAGGGCGCGCATTCCGTCTTGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGATGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAATCGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGATCAGGTTTACCAACGCAAACCGAACGAAA  >  NC_002947/3968831‑3969069

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑