BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524934.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 = 2,719,796 number of mapped reads = 2,516,346 (92.52%) number of supplementary alignments = 9,828 (0.36%) number of secondary alignments = 0 number of mapped bases = 147,003,548 bp number of sequenced bases = 146,955,765 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 172,548 duplication rate = 5.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9859 >>>>>>> ACTG content number of A's = 36,406,375 bp (24.77%) number of C's = 27,694,103 bp (18.85%) number of T's = 47,139,839 bp (32.08%) number of G's = 35,714,344 bp (24.3%) number of N's = 1,104 bp (0%) GC percentage = 43.15% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 739,172 number of insertions = 10,109 mapped reads with insertion percentage = 0.4% number of deletions = 28,743 mapped reads with deletion percentage = 1.13% homopolymer indels = 43.18% >>>>>>> Coverage mean coverageData = 0.0475X std coverageData = 0.4145X There is a 3.93% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% 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 14490515 0.058136324563058964 0.8195691105311868 chr2 243199373 12914004 0.05310048229441776 0.4871460524484624 chr3 198022430 9209817 0.04650895860635586 0.2554566026555491 chr4 191154276 6556537 0.03429971401738353 0.28886423347306406 chr5 180915260 9005892 0.049779615052925885 0.26135619206400085 chr6 171115067 9323311 0.05448562282361728 0.29543951407759333 chr7 159138663 8669895 0.05448012969670356 0.5190051764721264 chr8 146364022 12711825 0.08685074942802543 0.5468520117853353 chr9 141213431 5369666 0.03802517906388097 0.3189975958556919 chr10 135534747 6423170 0.047391315822502694 0.46097766864733447 chr11 135006516 9234316 0.06839903934710825 0.3680480190765181 chr12 133851895 4879158 0.03645191575360214 0.23152167008726274 chr13 115169878 3542977 0.03076305247106366 0.2064607660418877 chr14 107349540 2702699 0.025176623951998305 0.20161074258883357 chr15 102531392 3679905 0.03589052024183969 0.22359213573664408 chr16 90354753 4306522 0.04766237366616452 0.28084740868701924 chr17 81195210 3238018 0.03987942145848259 0.24657356984915998 chr18 78077248 3774201 0.04833931902927726 0.5541886421805615 chr19 59128983 3044852 0.05149508490616184 0.5441526303062693 chr20 63025520 2809047 0.0445699932344866 0.2607773412833831 chr21 48129895 1338341 0.027806854762512986 0.25779222044127875 chr22 51304566 2700232 0.05263141686063576 0.2731417267630128 chrMT 16571 20072 1.211272705328586 1.385245565688418 chrX 155270560 6619881 0.04263448911371222 0.2709928769356151 chrY 59373566 438695 0.007388725817815962 0.2589081292192598