BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717051.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 = 973,247 number of mapped reads = 759,285 (78.02%) number of supplementary alignments = 2,830 (0.29%) number of secondary alignments = 0 number of mapped bases = 42,725,718 bp number of sequenced bases = 42,713,875 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,955 duplication rate = 1.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.9572 >>>>>>> ACTG content number of A's = 10,340,930 bp (24.21%) number of C's = 9,244,041 bp (21.64%) number of T's = 12,417,828 bp (29.07%) number of G's = 10,709,930 bp (25.07%) number of N's = 1,146 bp (0%) GC percentage = 46.72% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 219,106 number of insertions = 3,634 mapped reads with insertion percentage = 0.48% number of deletions = 7,028 mapped reads with deletion percentage = 0.91% homopolymer indels = 32.42% >>>>>>> Coverage mean coverageData = 0.0138X std coverageData = 0.1421X There is a 1.28% of reference with a coverageData >= 1X There is a 0.07% 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 4117569 0.016519794347874463 0.16904464591233895 chr2 243199373 3684994 0.0151521525509854 0.16588283844316146 chr3 198022430 2870235 0.014494494386317752 0.13105742329823822 chr4 191154276 2750669 0.01438978534804003 0.1453005607820966 chr5 180915260 2634703 0.01456318831258347 0.12794519791517192 chr6 171115067 1825499 0.010668254011787285 0.11233211430802154 chr7 159138663 2461407 0.015467058435698936 0.16119075782230682 chr8 146364022 2642068 0.018051348711912277 0.14805533373688765 chr9 141213431 1884889 0.013347802589684264 0.13128061574797176 chr10 135534747 2250782 0.016606678728665794 0.2086184709617939 chr11 135006516 1771402 0.013120862995975691 0.1381210831929122 chr12 133851895 2076710 0.015514983930559967 0.13380682943564473 chr13 115169878 744159 0.006461403041514032 0.08598792286118084 chr14 107349540 1371155 0.01277280741025998 0.12230364170676353 chr15 102531392 856263 0.008351227690344826 0.0983576623800099 chr16 90354753 1165780 0.01290225429535511 0.12758493365147863 chr17 81195210 1668499 0.020549229443461013 0.15854631703438823 chr18 78077248 1165435 0.014926691576014565 0.15656419400762833 chr19 59128983 1131170 0.019130550579569413 0.17081583614356757 chr20 63025520 1098042 0.01742218072932996 0.1466524392735205 chr21 48129895 596267 0.012388703528233336 0.1328880804817661 chr22 51304566 469638 0.009153922089507589 0.10456200324384865 chrMT 16571 1851 0.11170116468529359 0.33934563647727856 chrX 155270560 1351610 0.008704869744786133 0.10421585194509832 chrY 59373566 134922 0.0022724254089774563 0.08190791724428458