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
A8 F1 I2 R1	765	53.2	2691310	93.4%	2513683	103.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,544,384	C→T	pseudogene (381/381 nt)	yddK ←	pseudogene, leucine‑rich protein, putative glycoportein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,544,384	0	C	T	100.0%	170.1 / NA	53	pseudogene (381/381 nt)	yddK	pseudogene, leucine‑rich protein, putative glycoportein
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (27/26); total (27/26)

ACCTTCAAACGGGGTTAATCTTTGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCACTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTCATGTT  >  NC_000913/1544254‑1544506

aCCTTCAAACGGGGTTAATCTTTGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCGTTAAAAAgg                                                                                                                    >  2:920184/1‑139 (MQ=255)

  cTTCAAACGGGGTTAATCTTTGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGcc                                                                                                                  >  2:1180726/1‑139 (MQ=255)

                      tGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGAt                                                                                              <  2:832839/139‑1 (MQ=255)

                      tGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGAt                                                                                              <  2:1217754/139‑1 (MQ=255)

                               gTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGa                                                                                     <  1:163080/139‑1 (MQ=255)

                               gTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGa                                                                                     <  2:1019024/139‑1 (MQ=255)

                                  aTGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAAc                                                                                                            <  1:1153190/113‑1 (MQ=255)

                                  aTGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAAc                                                                                                            >  2:1153190/1‑113 (MQ=255)

                                     tttCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCa                                                                                                                 <  1:461702/105‑1 (MQ=255)

                                     tttCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCa                                                                                                                 >  2:461702/1‑105 (MQ=255)

                                             cTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTc                                                                       <  1:1180726/139‑1 (MQ=255)

                                                                     tACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGGAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGtaata                                               >  2:1031944/1‑139 (MQ=255)

                                                                     tACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGAt                                                                                              <  2:1216411/92‑1 (MQ=255)

                                                                     tACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGAt                                                                                              >  1:1216411/1‑92 (MQ=255)

                                                                     tACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGtaata                                               >  2:1001476/1‑139 (MQ=255)

                                                                         tatTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTAt                                                                             >  2:89204/1‑105 (MQ=255)

                                                                         tatTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTAt                                                                             <  1:89204/105‑1 (MQ=255)

                                                                           ttAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGtt                                         <  1:1001476/139‑1 (MQ=255)

                                                                            tAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGtta                                        >  1:188483/1‑139 (MQ=255)

                                                                                  tattatCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGAt                                                                                              >  2:576523/1‑79 (MQ=255)

                                                                                  tattatCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGAt                                                                                              <  1:576523/79‑1 (MQ=255)

                                                                                     tatCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCct                                                                     <  2:1234758/101‑1 (MQ=255)

                                                                                     tatCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCct                                                                     >  1:1234758/1‑101 (MQ=255)

                                                                                       tCAACAAGACCAGACACTTATAGAATTAGTGATGACTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACagtaagt                             <  1:813939/139‑1 (MQ=255)

                                                                                         aacaaGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGa                                                                                               >  1:39871/1‑71 (MQ=255)

                                                                                         aacaaGACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGa                                                                                               <  2:39871/71‑1 (MQ=255)

                                                                                          acaaGACCAGACACTTATAGAATTAGTGATGATTTATTCATTaaaa                                                                                                                       <  2:11715/46‑1 (MQ=255)

                                                                                          acaaGACCAGACACTTATAGAATTAGTGATGATTTATTCATTaaaa                                                                                                                       >  1:11715/1‑46 (MQ=255)

                                                                                              gACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTAt                                                                             <  1:704057/84‑1 (MQ=255)

                                                                                              gACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTAt                                                                             >  2:704057/1‑84 (MQ=255)

                                                                                              gACCAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGttt                      >  2:20805/1‑139 (MQ=255)

                                                                                                ccAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGGAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTAt                    <  1:1031944/139‑1 (MQ=255)

                                                                                                ccAGACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCACGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTAt                    <  1:1287005/139‑1 (MQ=255)

                                                                                                   gACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACg                                                                                                <  1:1280051/60‑1 (MQ=255)

                                                                                                   gACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACg                                                                                                >  2:1280051/1‑60 (MQ=255)

                                                                                                   gACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATc                                                                                             >  1:778161/1‑63 (MQ=255)

                                                                                                   gACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATc                                                                                             <  2:778161/63‑1 (MQ=255)

                                                                                                   gACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTAt                                                                             <  1:144937/79‑1 (MQ=255)

                                                                                                   gACACTTATAGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTAt                                                                             >  2:144937/1‑79 (MQ=255)

                                                                                                         tataGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCt                                                         >  1:452494/1‑93 (MQ=255)

                                                                                                         tataGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCt                                                         <  2:452494/93‑1 (MQ=255)

                                                                                                          ataGAATTAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAg          >  1:992404/1‑139 (MQ=255)

                                                                                                                 tAGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTCATGt   >  1:1052004/1‑139 (MQ=255)

                                                                                                                  aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTaataat                                             <  2:1338421/96‑1 (MQ=255)

                                                                                                                  aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTaataat                                             >  1:1338421/1‑96 (MQ=255)

                                                                                                                  aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGttatt                                      <  1:552642/103‑1 (MQ=255)

                                                                                                                  aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGttatt                                      >  2:552642/1‑103 (MQ=255)

                                                                                                                  aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTCATGtt  >  1:698956/1‑139 (MQ=255)

                                                                                                                  aGTGATGATTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTCATGtt  >  1:1045753/1‑139 (MQ=255)

                                                                                                                    tgatgaTTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCt                                                         >  1:582621/1‑82 (MQ=255)

                                                                                                                    tgatgaTTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCt                                                         <  2:582621/82‑1 (MQ=255)

                                                                                                                        gatTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTAc                                    <  1:1073427/99‑1 (MQ=255)

                                                                                                                        gatTTATTCATTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTAc                                    >  2:1073427/1‑99 (MQ=255)

ACCTTCAAACGGGGTTAATCTTTGAACGTATGTCATGTTTCAACCCTTCAGATCGTGAATCTAAAGGGTTACATATTAACTATATTATCAACAAGACCAGACACTTATAGAATTAGTGATGATTTATTCACTAAAAAGGCCATGAACTGGAGGAAAACGATCTGTCCAGAAGGTCTATCGGTTCCTCTCTTATTGCCTGATTGTAATAATCGTTATTACAGTAAGTATTGTTTATTTCATCTAAGGTCATGTT  >  NC_000913/1544254‑1544506

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A