BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716686.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 = 1,056,926 number of mapped reads = 927,463 (87.75%) number of supplementary alignments = 3,607 (0.34%) number of secondary alignments = 0 number of mapped bases = 52,770,837 bp number of sequenced bases = 52,754,754 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,634 duplication rate = 1.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2832 >>>>>>> ACTG content number of A's = 12,926,248 bp (24.5%) number of C's = 10,208,949 bp (19.35%) number of T's = 16,683,325 bp (31.62%) number of G's = 12,935,836 bp (24.52%) number of N's = 396 bp (0%) GC percentage = 43.87% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 271,680 number of insertions = 3,753 mapped reads with insertion percentage = 0.4% number of deletions = 10,060 mapped reads with deletion percentage = 1.08% homopolymer indels = 41.92% >>>>>>> Coverage mean coverageData = 0.017X std coverageData = 0.1673X There is a 1.59% of reference with a coverageData >= 1X There is a 0.08% 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 4432028 0.017781412067173947 0.20688735009656084 chr2 243199373 4150279 0.017065335937358688 0.22576001662335446 chr3 198022430 3080304 0.015555328757454396 0.13285213669697687 chr4 191154276 3218820 0.01683885951889457 0.14406028214771285 chr5 180915260 3044978 0.01683096273912991 0.13582334540086968 chr6 171115067 2841729 0.016607123205579555 0.1518639699177496 chr7 159138663 3004603 0.01888040871626526 0.22383543122739344 chr8 146364022 2741269 0.01872911773359166 0.1697440402693192 chr9 141213431 1753484 0.012417260791574422 0.13006997165445505 chr10 135534747 2346091 0.0173098858553224 0.20025068401764035 chr11 135006516 1851279 0.013712515920342689 0.14042931897491598 chr12 133851895 2649225 0.019792211384082384 0.14822912899466195 chr13 115169878 1621236 0.014076909936467936 0.12458104666420848 chr14 107349540 1785959 0.016636857503068946 0.13934471874832016 chr15 102531392 1908882 0.018617537153889415 0.14527094126494536 chr16 90354753 1825106 0.020199335833500646 0.1552621961567652 chr17 81195210 2358147 0.029042932458700457 0.18587826374544839 chr18 78077248 971786 0.012446468400115741 0.18261009654755717 chr19 59128983 1393126 0.023560797587200172 0.20251126124939237 chr20 63025520 1700358 0.026978880935849478 0.1781883081049668 chr21 48129895 534500 0.011105363932333532 0.11799420206115073 chr22 51304566 492290 0.00959544224582272 0.10284147708778349 chrMT 16571 3203 0.19328948162452478 0.4583881702041468 chrX 155270560 2897015 0.018657851172817305 0.14955493632254094 chrY 59373566 165140 0.0027813724376939057 0.08525525288593891