BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231753.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 = 2,862,224 number of mapped reads = 2,232,895 (78.01%) number of supplementary alignments = 20,371 (0.71%) number of secondary alignments = 0 number of mapped bases = 154,505,900 bp number of sequenced bases = 154,461,375 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 926,320 duplication rate = 14.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3184 >>>>>>> ACTG content number of A's = 32,443,315 bp (21%) number of C's = 22,537,610 bp (14.59%) number of T's = 35,015,897 bp (22.67%) number of G's = 64,435,054 bp (41.72%) number of N's = 29,499 bp (0.02%) GC percentage = 56.31% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 882,974 number of insertions = 9,541 mapped reads with insertion percentage = 0.42% number of deletions = 26,688 mapped reads with deletion percentage = 1.18% homopolymer indels = 46.62% >>>>>>> Coverage mean coverageData = 0.0499X std coverageData = 78.9643X There is a 0.79% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.28% of reference with a coverageData >= 5X There is a 0.23% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.12% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 7015115 0.028144824561941614 0.7017746656307852 chr2 243199373 46833812 0.19257373661074365 281.7158566554209 chr3 198022430 7451271 0.03762841916443506 0.6587734585711974 chr4 191154276 8075960 0.042248387893765976 0.6920109562441012 chr5 180915260 6158062 0.03403837796767393 0.6087789949069778 chr6 171115067 5862589 0.03426109168983933 0.8734156881834668 chr7 159138663 6597574 0.04145802079536134 0.7114977698336373 chr8 146364022 7884780 0.05387102576342156 0.8306277817432343 chr9 141213431 4607270 0.03262628750943669 0.6126538287566536 chr10 135534747 6177177 0.04557633475347838 0.7017602193924877 chr11 135006516 5912447 0.0437937899234434 0.7706510597573797 chr12 133851895 3433618 0.0256523674916967 0.8477248866782638 chr13 115169878 3942477 0.034231841419507275 0.6374734378640308 chr14 107349540 3361649 0.03131498281222258 0.6357352975799134 chr15 102531392 3783749 0.03690332225275943 0.9920175669975785 chr16 90354753 2654748 0.029381387385343193 0.5564043173850286 chr17 81195210 2715378 0.03344258854678743 0.6266439768633689 chr18 78077248 4032426 0.05164662053662547 0.9348987507326262 chr19 59128983 2489120 0.04209644532529842 0.7305992497807184 chr20 63025520 3920964 0.06221232288127095 0.8104853574377848 chr21 48129895 3581876 0.07442102252664379 0.9291371884171167 chr22 51304566 3447749 0.06720160151047765 0.8292688605548386 chrMT 16571 352808 21.290688552290145 20.689265081490564 chrX 155270560 3866898 0.024904257445841634 0.5485567485774115 chrY 59373566 346383 0.005833959846710235 0.22148616490622977