BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716464.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 = 1,284,823 number of mapped reads = 1,134,411 (88.29%) number of supplementary alignments = 3,942 (0.31%) number of secondary alignments = 0 number of mapped bases = 64,756,377 bp number of sequenced bases = 64,736,480 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,575 duplication rate = 1.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2137 >>>>>>> ACTG content number of A's = 15,566,531 bp (24.05%) number of C's = 13,283,721 bp (20.52%) number of T's = 20,674,133 bp (31.94%) number of G's = 15,211,133 bp (23.5%) number of N's = 962 bp (0%) GC percentage = 44.02% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 327,844 number of insertions = 3,913 mapped reads with insertion percentage = 0.34% number of deletions = 12,476 mapped reads with deletion percentage = 1.09% homopolymer indels = 44.49% >>>>>>> Coverage mean coverageData = 0.0209X std coverageData = 0.2006X There is a 1.93% of reference with a coverageData >= 1X There is a 0.11% 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 5354400 0.02148199261658008 0.26989869408719386 chr2 243199373 6417448 0.02638760092527048 0.2750655568976716 chr3 198022430 4283067 0.021629201298054974 0.1569413437746679 chr4 191154276 3717799 0.01944920656653268 0.15272605224996538 chr5 180915260 3519677 0.01945483758528717 0.14780323221904787 chr6 171115067 3624654 0.02118255314127306 0.1674518234611436 chr7 159138663 3179041 0.019976547119790744 0.3202954093872411 chr8 146364022 5329906 0.03641541088560685 0.23840418154785087 chr9 141213431 2674550 0.018939770679461787 0.16602870217970814 chr10 135534747 3072408 0.02266878470655204 0.22572736259074544 chr11 135006516 2171973 0.01608791237898473 0.15395816692781952 chr12 133851895 3003539 0.02243927140516016 0.16006667275983938 chr13 115169878 1736198 0.015075104967984771 0.12969602801071067 chr14 107349540 2100837 0.01957006057035736 0.15083065397508605 chr15 102531392 1541283 0.015032303472481872 0.1317037969725379 chr16 90354753 1965117 0.021748905671846615 0.1651491431397318 chr17 81195210 2665965 0.03283401816437201 0.2001047036125247 chr18 78077248 1510166 0.01934194709321722 0.2506246015348303 chr19 59128983 1328523 0.022468220026716848 0.2467186700634209 chr20 63025520 1424898 0.022608270427598217 0.16080255945442937 chr21 48129895 660918 0.013731964302020606 0.12620685835313308 chr22 51304566 954862 0.01861163780237416 0.1455026111622595 chrMT 16571 54666 3.2988956610946834 2.6858369792739376 chrX 155270560 2318008 0.014928831325139807 0.14500006004299124 chrY 59373566 146474 0.0024669901080221456 0.07036125413750058