BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716461.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 = 566,260 number of mapped reads = 515,679 (91.07%) number of supplementary alignments = 1,710 (0.3%) number of secondary alignments = 0 number of mapped bases = 29,487,480 bp number of sequenced bases = 29,478,437 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,117 duplication rate = 1.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3042 >>>>>>> ACTG content number of A's = 7,185,554 bp (24.38%) number of C's = 5,147,574 bp (17.46%) number of T's = 9,856,258 bp (33.44%) number of G's = 7,288,518 bp (24.72%) number of N's = 533 bp (0%) GC percentage = 42.19% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 152,968 number of insertions = 2,299 mapped reads with insertion percentage = 0.44% number of deletions = 5,643 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.33% >>>>>>> Coverage mean coverageData = 0.0095X std coverageData = 0.125X There is a 0.91% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% 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 2475749 0.009932769635907949 0.17485469131286116 chr2 243199373 2341878 0.009629457391734311 0.16274692386056572 chr3 198022430 1682111 0.008494547814608679 0.09587361428342461 chr4 191154276 1849846 0.009677241015524026 0.10662711846510976 chr5 180915260 1693524 0.009360868729370867 0.09968598035636764 chr6 171115067 1598328 0.009340661976890673 0.10766930530033192 chr7 159138663 1711529 0.010754953998828053 0.16440776308313473 chr8 146364022 1560951 0.010664854509122468 0.14800275605832075 chr9 141213431 979520 0.006936450683646373 0.0957062885473093 chr10 135534747 1287625 0.009500331306185269 0.12784335929483626 chr11 135006516 1040257 0.007705235501373874 0.10138165269175413 chr12 133851895 1472501 0.011000972380704807 0.10875754948363299 chr13 115169878 895100 0.007771997466212476 0.09158522524117682 chr14 107349540 989425 0.009216853653960697 0.1001427924237182 chr15 102531392 1059637 0.010334756793314578 0.10662623313219391 chr16 90354753 980850 0.010855544035408962 0.11023462293736203 chr17 81195210 1244124 0.01532262802202248 0.12922640166079713 chr18 78077248 552674 0.0070785537932894355 0.13262725454432395 chr19 59128983 750725 0.012696396283359043 0.15803045191164536 chr20 63025520 963469 0.015286966295557735 0.12917328881722065 chr21 48129895 371953 0.0077281074475645545 0.09593036373095126 chr22 51304566 258520 0.005038927724288712 0.07349336869785413 chrMT 16571 8780 0.5298412889988534 0.8154116216009979 chrX 155270560 1616213 0.010409011212428165 0.11002798937982321 chrY 59373566 102191 0.001721153147513491 0.07657111125413808