BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716135.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 = 1,055,289 number of mapped reads = 975,942 (92.48%) number of supplementary alignments = 3,013 (0.29%) number of secondary alignments = 0 number of mapped bases = 56,677,396 bp number of sequenced bases = 56,659,693 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,136 duplication rate = 1.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.116 >>>>>>> ACTG content number of A's = 14,365,456 bp (25.35%) number of C's = 10,603,397 bp (18.71%) number of T's = 17,323,272 bp (30.57%) number of G's = 14,367,024 bp (25.36%) number of N's = 544 bp (0%) GC percentage = 44.07% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 274,358 number of insertions = 3,394 mapped reads with insertion percentage = 0.35% number of deletions = 11,206 mapped reads with deletion percentage = 1.14% homopolymer indels = 42.68% >>>>>>> Coverage mean coverageData = 0.0183X std coverageData = 0.1828X There is a 1.69% of reference with a coverageData >= 1X There is a 0.1% 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 6805455 0.0273036631672023 0.26682165172010763 chr2 243199373 5996310 0.024655943500314862 0.24426662186690853 chr3 198022430 3654047 0.018452692455092082 0.14643836501613142 chr4 191154276 2388456 0.012494912747858175 0.12395777357302261 chr5 180915260 4013392 0.02218382241498036 0.1579145865888382 chr6 171115067 2129987 0.012447688198024082 0.12886408307161334 chr7 159138663 3582653 0.02251277554091302 0.2594237624285343 chr8 146364022 2650527 0.01810914296957486 0.16268690852054923 chr9 141213431 1614326 0.011431816283820765 0.1395101114539868 chr10 135534747 2396171 0.01767938519854248 0.22418617026564758 chr11 135006516 2195234 0.016260207766564394 0.16907237242338216 chr12 133851895 2274382 0.016991780355444353 0.13850809341046327 chr13 115169878 1677210 0.014562922433589797 0.12850190232045897 chr14 107349540 1332698 0.012414566471360753 0.12213186956189281 chr15 102531392 2440326 0.023800769231729538 0.16355844073450265 chr16 90354753 1742612 0.019286334610421656 0.1617106939889059 chr17 81195210 2070346 0.025498376074155112 0.1794383509015832 chr18 78077248 1849142 0.023683493557559814 0.27620439083015275 chr19 59128983 896211 0.015156881693703408 0.2090916523855569 chr20 63025520 1511416 0.023981015944017598 0.1647483616630225 chr21 48129895 732804 0.0152255474482128 0.13331065619463142 chr22 51304566 605632 0.011804641325686295 0.11496361786112591 chrMT 16571 243 0.014664172349284896 0.12020455232059792 chrX 155270560 1991137 0.012823660840793 0.1322049250302822 chrY 59373566 126679 0.002133592582261271 0.06036202652630671