BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716434.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 = 2,653,457 number of mapped reads = 2,316,974 (87.32%) number of supplementary alignments = 8,600 (0.32%) number of secondary alignments = 0 number of mapped bases = 131,300,932 bp number of sequenced bases = 131,263,168 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,717 duplication rate = 2.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2537 >>>>>>> ACTG content number of A's = 33,552,610 bp (25.56%) number of C's = 27,607,326 bp (21.03%) number of T's = 39,022,507 bp (29.73%) number of G's = 31,078,773 bp (23.68%) number of N's = 1,952 bp (0%) GC percentage = 44.71% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 669,434 number of insertions = 7,858 mapped reads with insertion percentage = 0.34% number of deletions = 24,226 mapped reads with deletion percentage = 1.04% homopolymer indels = 42.81% >>>>>>> Coverage mean coverageData = 0.0424X std coverageData = 0.3687X There is a 3.68% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.07% 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 0.01% 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 11101771 0.04454059514660146 0.40947915248299205 chr2 243199373 12009281 0.04938039457856661 0.4621851933929994 chr3 198022430 9823337 0.04960719348813162 0.27980412864738674 chr4 191154276 7422981 0.03883240885492931 0.23236324511967912 chr5 180915260 6731063 0.037205612174451175 0.21550237878002607 chr6 171115067 7478227 0.0437029136656914 0.2659312544284199 chr7 159138663 8356210 0.05250898708379874 0.9333278685359229 chr8 146364022 9221121 0.06300128183140526 0.34062479267371515 chr9 141213431 5481121 0.03881444534833234 0.26232031569120245 chr10 135534747 6297395 0.04646332500993269 0.45967211437221484 chr11 135006516 3979216 0.02947425145020408 0.24710136564700516 chr12 133851895 6307567 0.04712347927535878 0.2610158826849589 chr13 115169878 3501559 0.030403427187792976 0.19408946020791984 chr14 107349540 3327732 0.030999033624177618 0.20780300737004695 chr15 102531392 3194236 0.031153736798969822 0.2059023961987706 chr16 90354753 4164366 0.04608906406949062 0.2564769153056826 chr17 81195210 5687199 0.07004352842981747 0.31765904677000173 chr18 78077248 3015824 0.03862615649567976 0.39841565899392845 chr19 59128983 2819019 0.047675756574402775 0.4283992305473221 chr20 63025520 2973893 0.04718553690631985 0.2523250211534047 chr21 48129895 1369756 0.02845956759307287 0.20021412075354528 chr22 51304566 1945100 0.037912804875885706 0.2223627387996704 chrMT 16571 65846 3.973568281938326 3.3450753152727697 chrX 155270560 4739522 0.03052427968315436 0.23603334748359203 chrY 59373566 287590 0.0048437380365531696 0.11020078694834211