BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524855.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 = 1,661,613 number of mapped reads = 1,520,588 (91.51%) number of supplementary alignments = 6,957 (0.42%) number of secondary alignments = 0 number of mapped bases = 88,229,208 bp number of sequenced bases = 88,198,507 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,449 duplication rate = 2.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9915 >>>>>>> ACTG content number of A's = 21,424,044 bp (24.29%) number of C's = 15,261,415 bp (17.3%) number of T's = 29,561,764 bp (33.52%) number of G's = 21,949,418 bp (24.89%) number of N's = 1,866 bp (0%) GC percentage = 42.19% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 449,231 number of insertions = 5,177 mapped reads with insertion percentage = 0.34% number of deletions = 18,998 mapped reads with deletion percentage = 1.24% homopolymer indels = 45.71% >>>>>>> Coverage mean coverageData = 0.0285X std coverageData = 0.2864X There is a 2.59% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 9698584 0.038910972261930694 0.5104765821083521 chr2 243199373 7708942 0.03169803402412555 0.3718093009876001 chr3 198022430 6789743 0.03428774710016436 0.20188344058380037 chr4 191154276 3995073 0.020899731272555996 0.16622434661362018 chr5 180915260 4180828 0.023109316483308263 0.1634948428795769 chr6 171115067 5656363 0.03305590266928394 0.2228434621226835 chr7 159138663 6228871 0.039141154528865185 0.5107264063093891 chr8 146364022 4412145 0.030145010636562036 0.24040911570795678 chr9 141213431 3051195 0.021606974481060515 0.20276388730763634 chr10 135534747 4880876 0.03601199034222567 0.31882441581277543 chr11 135006516 4122533 0.030535807619833696 0.24693405271856922 chr12 133851895 4044900 0.030219221027838267 0.1886061127704462 chr13 115169878 2065044 0.01793041753504332 0.14717169540485975 chr14 107349540 3443927 0.03208143230050171 0.1961667512280572 chr15 102531392 1772930 0.01729158226975013 0.14551536198988993 chr16 90354753 2385991 0.026406922942946897 0.19901284158203664 chr17 81195210 1552268 0.019117728742865495 0.15497608549367797 chr18 78077248 1997136 0.025578975324540128 0.3972913678996827 chr19 59128983 1419782 0.024011608655606337 0.3510668712377578 chr20 63025520 1532391 0.024313817640854055 0.1698445224150351 chr21 48129895 1148665 0.0238659361297173 0.17559226246267431 chr22 51304566 971596 0.018937807601763945 0.14728249154699774 chrMT 16571 4985 0.3008267455192807 0.5501017280507499 chrX 155270560 4921465 0.03169606009020641 0.21031129927620026 chrY 59373566 242975 0.004092309362048424 0.11304192492635334