BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524922.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 = 953,165 number of mapped reads = 826,163 (86.68%) number of supplementary alignments = 3,437 (0.36%) number of secondary alignments = 0 number of mapped bases = 47,391,591 bp number of sequenced bases = 47,379,447 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,508 duplication rate = 1.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1897 >>>>>>> ACTG content number of A's = 12,350,010 bp (26.07%) number of C's = 8,534,890 bp (18.01%) number of T's = 14,686,286 bp (31%) number of G's = 11,806,884 bp (24.92%) number of N's = 1,377 bp (0%) GC percentage = 42.93% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 222,510 number of insertions = 2,653 mapped reads with insertion percentage = 0.32% number of deletions = 7,222 mapped reads with deletion percentage = 0.87% homopolymer indels = 43.11% >>>>>>> Coverage mean coverageData = 0.0153X std coverageData = 0.1633X There is a 1.43% 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 3374494 0.013538558044354882 0.24776212493232824 chr2 243199373 3831507 0.015754592426519127 0.17254825940759147 chr3 198022430 2821490 0.014248335403216697 0.1245706023395017 chr4 191154276 2897790 0.015159430699839537 0.13767093928014826 chr5 180915260 2647839 0.014635796891870813 0.12729157510569522 chr6 171115067 2478767 0.01448596575075414 0.1320760207896538 chr7 159138663 2965534 0.018634905836804723 0.2067949267323367 chr8 146364022 2022603 0.013818990298039227 0.15604057563964127 chr9 141213431 2180154 0.015438715599226535 0.1628559656323686 chr10 135534747 1843264 0.013599936848666564 0.1571316168577375 chr11 135006516 1818041 0.013466320395972592 0.14415205359196626 chr12 133851895 3542889 0.026468725003855942 0.17999982061657407 chr13 115169878 1838864 0.015966535972192313 0.13193053137396374 chr14 107349540 1670778 0.015563904605459884 0.13458430578408037 chr15 102531392 1184049 0.011548160781821824 0.11288762452137799 chr16 90354753 1394988 0.015439010718119057 0.13344761053609835 chr17 81195210 1426723 0.017571516841941786 0.14134271102637888 chr18 78077248 1476420 0.018909734113579414 0.271199161436106 chr19 59128983 817446 0.01382479384094937 0.19192530262491375 chr20 63025520 1499097 0.02378555543849539 0.16436804413027675 chr21 48129895 597853 0.012421656020649952 0.124855278970568 chr22 51304566 475044 0.009259292827854737 0.10041670975120984 chrMT 16571 7022 0.4237523384225454 0.7064626233218562 chrX 155270560 2446009 0.01575320524380153 0.14200518033618556 chrY 59373566 132926 0.002238807754952768 0.0666041254211518