BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716698.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 = 1,325,875 number of mapped reads = 1,198,742 (90.41%) number of supplementary alignments = 19,355 (1.46%) number of secondary alignments = 0 number of mapped bases = 94,061,338 bp number of sequenced bases = 94,019,490 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,866 duplication rate = 2.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3725 >>>>>>> ACTG content number of A's = 23,342,346 bp (24.83%) number of C's = 17,672,301 bp (18.8%) number of T's = 28,734,455 bp (30.56%) number of G's = 24,264,766 bp (25.81%) number of N's = 5,622 bp (0.01%) GC percentage = 44.6% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 802,509 number of insertions = 9,424 mapped reads with insertion percentage = 0.77% number of deletions = 23,875 mapped reads with deletion percentage = 1.96% homopolymer indels = 43.24% >>>>>>> Coverage mean coverageData = 0.0304X std coverageData = 0.3953X There is a 2.71% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 7578319 0.030404413716586087 0.6311743858511714 chr2 243199373 8055092 0.03312135183835363 0.5822806033977238 chr3 198022430 6067666 0.030641306643898875 0.19233622642209103 chr4 191154276 5851462 0.03061120118495283 0.22361554215108356 chr5 180915260 5535985 0.030599878639314338 0.19604767925764924 chr6 171115067 5277697 0.03084297071280111 0.24411401500345278 chr7 159138663 5234555 0.03289304372250507 0.5263986398924736 chr8 146364022 4673928 0.031933585427161876 0.5070341153924783 chr9 141213431 4019750 0.02846577674329009 0.42999599002390254 chr10 135534747 4494413 0.033160596079468835 0.4130218114613962 chr11 135006516 4273149 0.03165142784663816 0.37867865180065446 chr12 133851895 4251511 0.03176280022034802 0.20017219045570353 chr13 115169878 2821030 0.02449451235851791 0.1686495483913894 chr14 107349540 2797922 0.026063660822393836 0.2549541359713578 chr15 102531392 2682134 0.026159149385195122 0.177085012855025 chr16 90354753 2865600 0.03171498902774932 0.23212033366060802 chr17 81195210 2775430 0.034182188826163515 0.22265060151191232 chr18 78077248 2570834 0.032926800903638406 0.8331050377563145 chr19 59128983 2288699 0.038706889310103645 0.5069155775175894 chr20 63025520 1935415 0.0307084336630622 0.2041805753230926 chr21 48129895 1214355 0.025230784318145717 0.20184431077799916 chr22 51304566 1149107 0.02239775305769081 0.16238129714638258 chrMT 16571 14601 0.8811176151107356 1.132502306041725 chrX 155270560 5339508 0.03438841207244953 0.2883274935424531 chrY 59373566 293176 0.004937820308788594 0.16179170841975116