Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,415,779	A→C	S42R (AGC→CGC)	rpsR →	30S ribosomal protein S18

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,415,779	0	A	C	100.0%	133.3 / NA	37	S42R (AGC→CGC)	rpsR	30S ribosomal protein S18
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (16/21);  total (16/21)

GACTAGCCATATGGCACGTTATTTCCGTCGTCGCAAGTTCTGCCGTTTCACCGCGGAAGGCGTTCAAGAGATCGACTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCAAGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAACGCGCTCGCTACCTGTCCCTGCTGCCGTACACTGATCGCCATCAGTAATCGGTCACGGTCCATTAATACGACTTTGA  >  NZ_CP009273/4415646‑4415912                                                                                                                                      |                                                                                                                                      gaCTAGCCATATGGCACGTTATTTCCGTCGTCGCAAGTTCTGCCGTTTCACCGCGGAAGGCGTTCAAGAGATCGACTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGt                                                                                                                                  <  1:6705/139‑1 (MQ=255)  aCTAGCCATATGGCACGTTATTTCCGTCGTCGCAAGTTCTGCCGTTTCACCGCGGAAGGCGTTCAAGAGATCGACTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTa                                                                                                                                 <  2:21553/139‑1 (MQ=255)    tAGCCATATGGCACGTTATTTCCGTCGTCGCAAGTTCTGCCGTTTCACCGCGGAAGGCGTTCAAGAGATCGACTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTAt                                                                                                                                >  1:342093/1‑138 (MQ=255)               cACGTTATTTCCGTCGTCGCAAGTTCTGCCGTTTCACCGCGGAAGGCGTTCAAGAGATCGACTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCg                                                                                                                    <  2:253177/139‑1 (MQ=255)               cACGTTATTTCCGTCGTCGCAAGTTCTGCCGTTTCACCGCGGAAGGCGTTCAAGAGATCGACTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCg                                                                                                                    <  1:2836/139‑1 (MQ=255)                 cGTTATTTCCGTCGTCGCAAGTTCTGCCGTTTCACCGCGGAAGGCGTTCAAGAGATCGACTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTa                                                                                                                                 >  2:230994/1‑124 (MQ=255)                 cGTTATTTCCGTCGTCGCAAGTTCTGCCGTTTCACCGCGGAAGGCGTTCAAGAGATCGACTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTa                                                                                                                                 <  1:230994/124‑1 (MQ=255)                 cGTTATTTCCGTCGTCGCAAGTTCTGCCGTTTCACCGCGGAAGGCGTTCAAGAGATCGACTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTg                                                                                                                  >  2:385840/1‑139 (MQ=255)                 cGTTATTTCCGTCGTCGCAAGTTCTGCCGTTTCACCGCGGAAGGCGTTCAAGAGATCGACTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTg                                                                                                                  >  1:417172/1‑139 (MQ=255)                         ccGTCGTCGCAAGTTCTGCCGTTTCACCGCGGAAGGCGTTCAAGAGATCGACTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATAc                                                                                                          >  2:209428/1‑139 (MQ=255)                                cgCAAGTTCTGCCGTTTCACCGCGGAAGGCGTTCAAGAGATCGACTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGt                                                                                                    >  1:172027/1‑138 (MQ=255)                                cgCAAGTTCTGCCGTTTCACCGCGGAAGGCGTTCAAGAGATCGACTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGt                                                                                                    >  2:91969/1‑138 (MQ=255)                                      ttCTGCCGTTTCACCGCGGAAGGCGTTCAAGAGATCGACTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTgg                                                                                             >  1:320233/1‑139 (MQ=255)                                         tGCCGTTTCACCGCGGAAGGCGTTCAAGAGATCGACTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGc                                                                                                      <  2:306822/127‑1 (MQ=255)                                         tGCCGTTTCACCGCGGAAGGCGTTCAAGAGATCGACTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGc                                                                                                      >  1:306822/1‑127 (MQ=255)                                                tCACCGCGGAAGGCGTTCAAGAGATCGACTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTAt                                                                                   >  2:234844/1‑139 (MQ=255)                                                        gaggccGTTCAAGAGATCGACTATAAAGATATCCCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAAcgcg                                                                           <  1:190498/134‑1 (MQ=255)                                                                 cAAGAGATCGACTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAACGCGCTCGCTAcc                                                                  >  2:347091/1‑139 (MQ=255)                                                                  aaGAGATCGACTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAACGCGCTCGCTAcc                                                                  <  1:47909/138‑1 (MQ=255)                                                                          gACTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAACGCGCTCGCTACCTGTCCctg                                                          <  2:388805/138‑1 (MQ=255)                                                                          gACTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAACGCGCTCGCTACCTGTCCctg                                                          <  1:234844/138‑1 (MQ=255)                                                                            cTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAACGCGCTCGCTACCTGTCCctgctg                                                       <  1:388317/139‑1 (MQ=255)                                                                            cTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAACGCGCTCGCTACCTGTCCctgctg                                                       <  1:347091/139‑1 (MQ=255)                                                                            cTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAACGCGCTCGCTACCTGTCCctgctg                                                       <  2:417172/139‑1 (MQ=255)                                                                              ataAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAACGcgct                                                                         <  2:194924/119‑1 (MQ=255)                                                                              ataAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAACGcgct                                                                         >  1:194924/1‑119 (MQ=255)                                                                                aaaGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAACGCGCTCGCTACCTGTCCCTGCTGCCg                                                    >  1:110933/1‑138 (MQ=255)                                                                                 aaGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAACGCGCTCGCTACCTGTCCCTGCTGCCGt                                                   <  2:320233/138‑1 (MQ=255)                                                                                 aaGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAACGCGCTCGCTACCTGTCCCTGCTGCCGTa                                                  <  1:147422/139‑1 (MQ=255)                                                                                         gCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAACGCGCTCGCTACCTGTCCCTGCTGCCGTACACTGATc                                          >  1:70958/1‑139 (MQ=255)                                                                                                  aaaaaCTACATCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAACGCGCTCGCTACCTGTCCCTGCTGCCGTACACTGATCGCCATCAg                                  <  1:91969/138‑1 (MQ=255)                                                                                                           aTCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAACGCGCTCGCTACCTGTCCCTGCTGCCGTACACTGATCGCCATCAGTAATCGGTCa                        <  1:354962/139‑1 (MQ=255)                                                                                                            tCACCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAACGCGCTCGCTACCTGTCCCTGCTGCCGTACACTGATCGCCATCAGTAATCGGTCAc                       >  2:434037/1‑139 (MQ=255)                                                                                                              aCCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAACGCGCTCGCTACCTGTCCCTGCTGCCGTACACTGATCGCCATCAGTAATCGGTCACgg                     <  2:342093/139‑1 (MQ=255)                                                                                                              aCCGAAAGCGGTAAGATTGTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAACGCGCTCGCTACCTGTCCCTGCTGCCGTACACTGATCGCCATCAGTAATCGGTCACg                      <  2:437687/138‑1 (MQ=255)                                                                                                                                gTCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAACGCGCTCGCTACCTGTCCCTGCTGCCGTACACTGATCGCCATCAGTAATCGGTCACGGTCCATTAATACGACttt    >  2:24722/1‑138 (MQ=255)                                                                                                                                 tCCCACGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAACGCGCTCGCTACCTGTCCCTGCTGCCGTACACTGATCGCCATCAGTAATCGGTCACGGTCCATTAATACGACTTTga  <  2:172027/139‑1 (MQ=255)                                                                                                                                      |                                                                                                                                      GACTAGCCATATGGCACGTTATTTCCGTCGTCGCAAGTTCTGCCGTTTCACCGCGGAAGGCGTTCAAGAGATCGACTATAAAGATATCGCTACGCTGAAAAACTACATCACCGAAAGCGGTAAGATTGTCCCAAGCCGTATCACCGGTACCCGTGCAAAATACCAGCGTCAGCTGGCTCGCGCTATCAAACGCGCTCGCTACCTGTCCCTGCTGCCGTACACTGATCGCCATCAGTAATCGGTCACGGTCCATTAATACGACTTTGA  >  NZ_CP009273/4415646‑4415912

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑