BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240226.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,778,129 number of mapped reads = 1,506,059 (84.7%) number of supplementary alignments = 12,534 (0.7%) number of secondary alignments = 0 number of mapped bases = 97,703,464 bp number of sequenced bases = 97,665,130 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 163,993 duplication rate = 8.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4488 >>>>>>> ACTG content number of A's = 27,250,772 bp (27.9%) number of C's = 17,650,756 bp (18.07%) number of T's = 31,291,850 bp (32.04%) number of G's = 21,447,153 bp (21.96%) number of N's = 24,599 bp (0.03%) GC percentage = 40.03% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 759,253 number of insertions = 7,236 mapped reads with insertion percentage = 0.48% number of deletions = 22,273 mapped reads with deletion percentage = 1.46% homopolymer indels = 48.4% >>>>>>> Coverage mean coverageData = 0.0316X std coverageData = 0.3654X There is a 2.01% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 7691351 0.03085790105213018 0.6135744375921427 chr2 243199373 8624124 0.035461127607430136 0.4007381450227347 chr3 198022430 6354437 0.03208948097445325 0.26090532421416834 chr4 191154276 6730472 0.03520963350042978 0.28313915595427086 chr5 180915260 5934477 0.03280252312602044 0.26548769989266885 chr6 171115067 5961330 0.03483813614145387 0.30047029168409456 chr7 159138663 5711488 0.03589000870266203 0.48771136959452455 chr8 146364022 4743158 0.03240658418091298 0.5522598408703137 chr9 141213431 4006061 0.02836883837203842 0.32182335531019635 chr10 135534747 4723204 0.0348486576656243 0.32236888867230323 chr11 135006516 4244947 0.03144253422553323 0.30414954454206417 chr12 133851895 4577636 0.034199261803503044 0.2740621278784485 chr13 115169878 3114782 0.02704510983331944 0.24234358499315503 chr14 107349540 2925825 0.027255123776031086 0.25403155269550187 chr15 102531392 2863809 0.027931045742556584 0.2466166987808812 chr16 90354753 2527538 0.027973492440403216 0.24983542434747624 chr17 81195210 2356491 0.02902253716690923 0.25666575102630407 chr18 78077248 2594958 0.033235776957712446 0.5629217987368148 chr19 59128983 1704087 0.028819825972653715 0.4132869002913128 chr20 63025520 1994821 0.03165100422812854 0.26609865939047617 chr21 48129895 1311634 0.02725196055383042 0.24598072837950302 chr22 51304566 994402 0.01938232944022955 0.19567296792003777 chrMT 16571 22150 1.336672500150866 1.9081356034098944 chrX 155270560 5733411 0.03692529350058375 0.29742883264403785 chrY 59373566 256871 0.004326352909306475 0.10286641621849435