Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A1 F5 I97 R1	275	44.0	1733530	96.5%	1672856	122.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	716,126	A→G	intergenic (‑210/+48)	speF ← / ← BW25113_RS26090	ornithine decarboxylase SpeF/leader peptide SpeFL

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	716,126	0	A	G	100.0%	128.9 / NA	34	intergenic (‑210/+48)	speF/BW25113_RS26090	ornithine decarboxylase SpeF/leader peptide SpeFL
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (16/18); total (16/18)

GCAAAGTTACCCCGCTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATACAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTTATATGGGG  >  NZ_CP009273/715990‑716254

gCAAAGTTACCCCGCTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCa                                                                                                                                <  2:138352/139‑1 (MQ=255)

gCAAAGTTACCCCGCTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCa                                                                                                                                <  1:36735/139‑1 (MQ=255)

gCAAAGTTACCCCGCTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCa                                                                                                                                <  1:794653/139‑1 (MQ=255)

gCAAAGTTACCCCGCTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCa                                                                                                                                <  1:772323/139‑1 (MQ=255)

           ccGCTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTT‑ACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGaa                                                                                                                    <  2:577484/139‑1 (MQ=255)

                      taaatCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACg                                                                                                          <  1:3861/139‑1 (MQ=255)

                                   ttGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCtt                                                                                             <  1:766097/139‑1 (MQ=255)

                                            tCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTa                                                                                     <  1:145289/138‑1 (MQ=255)

                                                aaTGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGAc                                                                                                                 >  1:533265/1‑106 (MQ=255)

                                                aaTGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGAc                                                                                                                 <  2:533265/106‑1 (MQ=255)

                                                             ttACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTg                                                                      >  2:18108/1‑136 (MQ=255)

                                                                    tCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAg                                                                                                    >  1:4630/1‑99 (MQ=255)

                                                                    tCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAg                                                                                                    <  2:4630/99‑1 (MQ=255)

                                                                     cAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGCGCATTGAAGAAGTGa                                                             >  2:460184/1‑137 (MQ=255)

                                                                             tGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGc                                                   >  1:531180/1‑139 (MQ=255)

                                                                                             aaCAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTgaa                                                                    >  1:680021/1‑106 (MQ=255)

                                                                                             aaCAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTgaa                                                                    <  2:680021/106‑1 (MQ=255)

                                                                                             aaCAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCaaa                                   >  2:728625/1‑139 (MQ=255)

                                                                                                  agaATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCa                              >  2:593587/1‑139 (MQ=255)

                                                                                                   gaATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAg                                       <  1:608754/129‑1 (MQ=255)

                                                                                                   gaATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAg                                       >  2:608754/1‑129 (MQ=255)

                                                                                                    aaTGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCat                             >  2:754040/1‑138 (MQ=255)

                                                                                                    aaTGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCat                             >  2:338974/1‑138 (MQ=255)

                                                                                                    aaTGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCat                             >  1:22330/1‑138 (MQ=255)

                                                                                                            cTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGt                    >  2:420541/1‑139 (MQ=255)

                                                                                                                gtaaTACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGCCCTGTACGCTGAAGGGCCCTTAGTCGTTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTc                <  2:703481/137‑1 (MQ=255)

                                                                                                                    tACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGcc            <  2:385918/139‑1 (MQ=255)

                                                                                                                    tACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGcc            <  2:22330/139‑1 (MQ=255)

                                                                                                                    tACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGcc            <  1:618559/139‑1 (MQ=255)

                                                                                                                       aGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTta         >  1:103234/1‑139 (MQ=255)

                                                                                                                         gCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTtata       <  1:754040/139‑1 (MQ=255)

                                                                                                                              tGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTTATATgggg  >  1:752281/1‑139 (MQ=255)

                                                                                                                                    tAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTc                >  2:575538/1‑119 (MQ=255)

                                                                                                                                    tAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTc                <  1:575538/119‑1 (MQ=255)

GCAAAGTTACCCCGCTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATACAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTTATATGGGG  >  NZ_CP009273/715990‑716254

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

AGCAAAGTTACCCCGCTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATACAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTTATATGGGGCATAGTGCGGCT  >  NZ_CP009273/715989‑716266

AGCAAAGTTACCCCGCTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGA                                                                                                                                 <  SRR3722120.805335/151‑1 (MQ=60)

AGCAAAGTTACCCCGCTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGA                                                                                                                                 <  SRR3722120.782759/151‑1 (MQ=60)

AGCAAAGTTACCCCGCTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGA                                                                                                                                 <  SRR3722120.37174/151‑1 (MQ=60)

                      ATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCC                                                                                                           <  SRR3722120.3905/151‑1 (MQ=60)

                                   ATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGAC                                                                                              <  SRR3722120.776420/151‑1 (MQ=60)

                                      GCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGActgtctcttatacacatctccg                                                                                            >  SRR3722120.540832/1‑128 (MQ=60)

                                            TTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGC                                                                                      <  SRR3722120.147249/150‑1 (MQ=60)

                                                          ACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCctgtctcttatacacatctccgagcccacg                                                                       >  SRR3722120.4686/1‑121 (MQ=60)

                                                                   AGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCT                                                              >  SRR3722120.538730/1‑151 (MQ=60)

                                                                                   ATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCtgtctcttatacacatctccg                                               >  SRR3722120.689358/1‑129 (MQ=60)

                                                                                         GGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATA                                        <  SRR3722120.617191/151‑1 (MQ=60)

                                                                                          GGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATA                                        >  SRR3722120.22581/1‑150 (MQ=60)

                                                                                                             CTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTTAT                    >  SRR3722120.104612/1‑151 (MQ=60)

                                                                                                               agatgtgtataagagacagCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTTATAT                  <  SRR3722120.227371/132‑1 (MQ=60)

                                                                                                                gagatgtgtataagagacagGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTTATATG                 <  SRR3722120.212674/131‑1 (MQ=60)

                                                                                                                 aagagACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTTATATG                 <  SRR3722120.583549/145‑1 (MQ=60)

                                                                                                                  gtataagagacagTGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTTATATGG                <  SRR3722120.854098/137‑1 (MQ=60)

                                                                                                                    ATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTTATATGGGGC             <  SRR3722120.627163/151‑1 (MQ=60)

                                                                                                                    ATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTTATATGGGGC             >  SRR3722120.762453/1‑151 (MQ=60)

                                                                                                                         GGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTTATATGGGGCATAGT        <  SRR3722120.764232/151‑1 (MQ=60)

                                                                                                                               TGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGActgtctcttatacacatctccgagcccacgagactaaggcgaatatcgtatgc  >  SRR3722120.205277/1‑98 (MQ=60)

AGCAAAGTTACCCCGCTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATACAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTTATATGGGGCATAGTGCGGCT  >  NZ_CP009273/715989‑716266

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`