Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	257,908	Δ776 bp		insB9–[crl]	insB9, insA9, [crl]

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	257908–258676	258683	8–776	69 [0]	[0] 69	insB9–[crl]	insB9,insA9,[crl]

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 257907	0 (0.000)	60 (1.370)	21/112	0.3	100%	intergenic (+8/+16)	crl/insB9	RNA polymerase holoenzyme assembly factor Crl/IS1 transposase B
	?	NC_000913	258684 =	0 (0.000)					pseudogene (9/331 nt)	crl	RNA polymerase holoenzyme assembly factor Crl

CTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACC  >  NC_000913/258620‑258747                                                                 |                                                                ggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaa                                                                 >  1:3943379‑M2/65‑65 (MQ=255) ggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaa                                                                 >  1:327013‑M2/65‑65 (MQ=255) ggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaa                                                                 >  1:2706661‑M2/65‑65 (MQ=255) ggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaa                                                                 >  1:3163904‑M2/65‑65 (MQ=255) ggacacccgaagagcagattgatcaaaaaacttaccgcactaggcccgtatactcgtgaacgtaa                                                                 >  1:2392159‑M2/65‑65 (MQ=255)  gacacccgaagagcagattgatcaaaaaatttaccgcactaggcccggatattcgtgaagggaAg                                                                >  1:545100‑M2/64‑65 (MQ=255)   acacctgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGt                                                               >  1:1946042‑M2/63‑65 (MQ=255)   acacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGt                                                               <  1:955427‑M2/3‑1 (MQ=255)   acacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGt                                                               <  1:1793720‑M2/3‑1 (MQ=255)    cacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTg                                                              >  1:3975169‑M2/62‑65 (MQ=255)    cacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTg                                                              >  1:2085872‑M2/62‑65 (MQ=255)      cccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCa                                                            >  1:3644827‑M2/60‑65 (MQ=255)      cccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggcaAGTGCa                                                            >  1:3544847‑M2/60‑65 (MQ=255)         gaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAg                                                         <  1:46535‑M2/9‑1 (MQ=255)           agagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGAt                                                       <  1:3952969‑M2/11‑1 (MQ=255)           agagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGAt                                                       >  1:3901464‑M2/55‑65 (MQ=255)           agagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGAt                                                       <  1:3431400‑M2/11‑1 (MQ=255)           agagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGAt                                                       >  1:1421666‑M2/55‑65 (MQ=255)             agcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATaa                                                     >  1:2285411‑M2/53‑65 (MQ=255)             agcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATaa                                                     >  1:2591091‑M2/53‑65 (MQ=255)             agcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATaa                                                     >  1:2612021‑M2/53‑65 (MQ=255)             agcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATaa                                                     >  1:2673005‑M2/53‑65 (MQ=255)             agcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATaa                                                     >  1:2394061‑M2/53‑65 (MQ=255)             agcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATaa                                                     >  1:2318351‑M2/53‑65 (MQ=255)             agcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATaa                                                     >  1:630241‑M2/53‑65 (MQ=255)             agcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATaa                                                     >  1:150692‑M2/53‑65 (MQ=255)             agcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATaa                                                     >  1:863710‑M2/53‑65 (MQ=255)             agcagattgatcaaaaaatttaccgcactaggcacgtatattcgtgaaggtaAGTGCAAAGATaa                                                     >  1:3411975‑M2/53‑65 (MQ=255)                  attgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGAt                                                <  1:503835‑M2/18‑1 (MQ=255)                  attgatcaaaaaagttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGAt                                                <  1:3943724‑M2/18‑1 (MQ=255)                   ttgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGAtt                                               >  1:2869801‑M2/47‑65 (MQ=255)                   ttgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGAtt                                               >  1:1092276‑M2/47‑65 (MQ=255)                                ttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGt                                  <  1:2339794‑M2/32‑1 (MQ=255)                                ttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGt                                  <  1:1943288‑M2/32‑1 (MQ=255)                                ttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGt                                  <  1:3192088‑M2/32‑1 (MQ=255)                                ttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGt                                  <  1:1837338‑M2/32‑1 (MQ=255)                                ttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGt                                  <  1:844323‑M2/32‑1 (MQ=255)                                tgaccgcacgaggcccgtatattcgtgaaggtaAGTGTAAAGATAATCGATTCTTTTTCGATTGt                                  <  1:561984‑M2/32‑1 (MQ=255)                                    cgcactaggtccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTgg                              <  1:1477341‑M2/36‑1 (MQ=255)                                    cgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTgg                              <  1:48995‑M2/36‑1 (MQ=255)                                    cgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTgg                              <  1:2359414‑M2/36‑1 (MQ=255)                                    cgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTgg                              <  1:3853855‑M2/36‑1 (MQ=255)                                    cgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTgg                              <  1:1733628‑M2/36‑1 (MQ=255)                                    cgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTgg                              <  1:3351264‑M2/36‑1 (MQ=255)                                     gcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGc                             <  1:1116605‑M2/37‑1 (MQ=255)                                      cactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCt                            <  1:3044856‑M2/38‑1 (MQ=255)                                      cactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCt                            <  1:531147‑M2/38‑1 (MQ=255)                                        ctaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGt                          <  1:897778‑M2/40‑1 (MQ=255)                                        ctaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGt                          <  1:3477395‑M2/40‑1 (MQ=255)                                        ctaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGt                          <  1:1265778‑M2/40‑1 (MQ=255)                                        ctaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGt                          <  1:2572190‑M2/40‑1 (MQ=255)                                        ctaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGt                          <  1:2415923‑M2/40‑1 (MQ=255)                                        ctaggcccgtatagtcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGt                          <  1:2552944‑M2/40‑1 (MQ=255)                                              ccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGt                    <  1:2636517‑M2/46‑1 (MQ=255)                                                 tatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCaa                 >  1:3211681‑M2/17‑65 (MQ=255)                                                  atattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAAc                <  1:3087857‑M2/50‑1 (MQ=255)                                                  atattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAAc                >  1:785740‑M2/16‑65 (MQ=255)                                                  atattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAAc                >  1:2421869‑M2/16‑65 (MQ=255)                                                  atattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAAc                <  1:190897‑M2/50‑1 (MQ=255)                                                     ttcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTg             >  1:2745329‑M2/13‑65 (MQ=255)                                                         tgaaggtaAGTGCAAAGATAATCGATTCCTTTTCGCTTGTCTGGCTGTATGCGTCAACGTGAAAc         >  1:3266242‑M2/9‑65 (MQ=255)                                                          gaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAAcc        <  1:1161516‑M2/58‑1 (MQ=255)                                                            aggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCgg      <  1:2288103‑M2/60‑1 (MQ=255)                                                              gtaAGTGCAAAGATAATCGATTCTTTTTGGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCa    <  1:2495682‑M2/62‑1 (MQ=255)                                                              gtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCa    <  1:1217953‑M2/62‑1 (MQ=255)                                                              gtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCa    <  1:3323454‑M2/62‑1 (MQ=255)                                                              gtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCa    >  1:980901‑M2/4‑65 (MQ=255)                                                                aAGTGCAAAGCTAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAGCCGGCAcc  <  1:323755‑M2/64‑1 (MQ=255)                                                                aAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCAcc  <  1:1871460‑M2/64‑1 (MQ=255)                                                                 |                                                                CTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACC  >  NC_000913/258620‑258747

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑