BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716620.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 = 1,326,973 number of mapped reads = 1,230,448 (92.73%) number of supplementary alignments = 27,444 (2.07%) number of secondary alignments = 0 number of mapped bases = 94,547,189 bp number of sequenced bases = 94,507,767 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,204 duplication rate = 3.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0914 >>>>>>> ACTG content number of A's = 23,749,507 bp (25.13%) number of C's = 18,617,164 bp (19.7%) number of T's = 28,080,881 bp (29.71%) number of G's = 24,056,924 bp (25.45%) number of N's = 3,291 bp (0%) GC percentage = 45.15% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 642,795 number of insertions = 8,103 mapped reads with insertion percentage = 0.65% number of deletions = 19,132 mapped reads with deletion percentage = 1.53% homopolymer indels = 39.09% >>>>>>> Coverage mean coverageData = 0.0305X std coverageData = 0.2821X There is a 2.63% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 10509947 0.04216618180461825 0.5317467395640788 chr2 243199373 8955734 0.03682465908331104 0.2986800248511506 chr3 198022430 6025517 0.030428457018732674 0.19823670708656768 chr4 191154276 4609565 0.024114370321488388 0.2447250967305676 chr5 180915260 4729771 0.026143571305151374 0.18343757999013602 chr6 171115067 5133063 0.02999772661749301 0.2072303535779068 chr7 159138663 5839802 0.036696311819585915 0.36800572606586546 chr8 146364022 5884689 0.0402058437557831 0.29349344576393105 chr9 141213431 2809021 0.01989202429335493 0.19455135123739467 chr10 135534747 4985245 0.03678204379575077 0.38009840384575544 chr11 135006516 4013637 0.02972920951459854 0.2517980954315923 chr12 133851895 3664650 0.027378394605470473 0.1869171636481325 chr13 115169878 1842222 0.015995692901576226 0.1400735306641528 chr14 107349540 1751198 0.016313046148125086 0.15389633044508505 chr15 102531392 1936449 0.018886401152146653 0.154612023051266 chr16 90354753 2730721 0.03022221752960799 0.20634704657497785 chr17 81195210 2340814 0.028829459274752785 0.20701152691611702 chr18 78077248 2658268 0.03404664057831547 0.28259225886336153 chr19 59128983 2325508 0.03932940974141226 0.3888976468652036 chr20 63025520 2509515 0.0398174422043642 0.23754715694169812 chr21 48129895 1475839 0.030663665482752456 0.2362404033059784 chr22 51304566 1421551 0.02770807962784443 0.1921292250621513 chrMT 16571 40845 2.4648482288335045 2.4736138552649187 chrX 155270560 6016382 0.03874773170136052 0.22929816217567564 chrY 59373566 337236 0.005679901389113128 0.21226524327604238