BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716913.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 717,442 number of mapped reads = 603,219 (84.08%) number of supplementary alignments = 2,269 (0.32%) number of secondary alignments = 0 number of mapped bases = 33,501,085 bp number of sequenced bases = 33,491,396 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,120 duplication rate = 1.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.657 >>>>>>> ACTG content number of A's = 7,362,187 bp (21.98%) number of C's = 7,234,444 bp (21.6%) number of T's = 9,842,901 bp (29.39%) number of G's = 9,051,008 bp (27.02%) number of N's = 856 bp (0%) GC percentage = 48.63% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 177,740 number of insertions = 2,307 mapped reads with insertion percentage = 0.38% number of deletions = 5,544 mapped reads with deletion percentage = 0.91% homopolymer indels = 33.87% >>>>>>> Coverage mean coverageData = 0.0108X std coverageData = 0.1187X There is a 1.01% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2746338 0.011018379769653613 0.1204750415272092 chr2 243199373 2710353 0.011144572317626823 0.13681166703239656 chr3 198022430 2100250 0.010606121740855316 0.11104968121779248 chr4 191154276 2067284 0.010814741073330737 0.12282084324668018 chr5 180915260 1946472 0.010759026076628361 0.11008931287814855 chr6 171115067 1843551 0.010773750274135708 0.11021920054927592 chr7 159138663 1831289 0.01150750525031117 0.12650656471030858 chr8 146364022 1623881 0.011094809898022617 0.116086226435078 chr9 141213431 1402646 0.009932808728370887 0.11121660468902404 chr10 135534747 1678102 0.012381341590581196 0.14829319161779786 chr11 135006516 1481239 0.010971611177641232 0.11973591991479869 chr12 133851895 1549306 0.01157477822783159 0.11434414630422984 chr13 115169878 1005384 0.008729574238152791 0.10113543339471727 chr14 107349540 1013788 0.009443803857939215 0.10431373638117178 chr15 102531392 980937 0.009567186993813563 0.10362405997984547 chr16 90354753 1121754 0.012414997139110102 0.12269103866834037 chr17 81195210 1084534 0.013357117987625133 0.12395877916685803 chr18 78077248 865551 0.011085828742324524 0.12712094171287167 chr19 59128983 893972 0.015119015322824003 0.13916365103531367 chr20 63025520 766838 0.012167103103631671 0.12059106215551635 chr21 48129895 451102 0.009372594725170292 0.11289998362440856 chr22 51304566 482782 0.009410117610194772 0.10419165245390814 chrMT 16571 2741 0.16540945024440287 0.4221367976600987 chrX 155270560 1726662 0.01112034374062926 0.11475318899190778 chrY 59373566 124329 0.002094012678975691 0.07376432021465418