BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173996.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 1,429,456 number of mapped reads = 1,387,317 (97.05%) number of supplementary alignments = 145,824 (10.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 695,757 number of mapped paired reads (second in pair) = 691,560 number of mapped paired reads (both in pair) = 1,359,066 number of mapped paired reads (singletons) = 28,251 number of mapped bases = 163,576,126 bp number of sequenced bases = 163,476,862 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,079,841 duplication rate = 63.81% >>>>>>> Insert size mean insert size = 1,136,681.193 std insert size = 9,772,332.9694 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 52.7651 >>>>>>> ACTG content number of A's = 49,067,356 bp (30.01%) number of C's = 32,119,567 bp (19.65%) number of T's = 48,894,232 bp (29.91%) number of G's = 33,393,698 bp (20.43%) number of N's = 2,009 bp (0%) GC percentage = 40.07% >>>>>>> Mismatches and indels general error rate = 0.0114 number of mismatches = 1,807,301 number of insertions = 19,930 mapped reads with insertion percentage = 1.38% number of deletions = 39,745 mapped reads with deletion percentage = 2.79% homopolymer indels = 42.23% >>>>>>> Coverage mean coverageData = 0.0528X std coverageData = 0.9785X There is a 1.13% of reference with a coverageData >= 1X There is a 0.88% of reference with a coverageData >= 2X There is a 0.68% of reference with a coverageData >= 3X There is a 0.56% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.34% of reference with a coverageData >= 6X There is a 0.25% of reference with a coverageData >= 7X There is a 0.2% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.08% 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 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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% 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 12007562 0.04817465229103682 0.811454288536409 chr2 243199373 15847200 0.06516135220463747 2.4352558424078694 chr3 198022430 10435522 0.052698686709379335 0.6639689200470327 chr4 191154276 11633531 0.06085938145584564 0.8148507608427837 chr5 180915260 10678945 0.05902733135944419 0.7014087144675654 chr6 171115067 9218403 0.05387253829611626 0.7063128155499846 chr7 159138663 8955099 0.056272302601913904 0.8018621212803526 chr8 146364022 8874165 0.06063078124486084 0.8733739924271984 chr9 141213431 7205149 0.05102311408324892 0.7806257246475259 chr10 135534747 8161608 0.06021782738857365 0.9061554262485892 chr11 135006516 7092515 0.052534612477519234 0.6673525876181693 chr12 133851895 7045576 0.052637103120579655 0.665737470905146 chr13 115169878 5162062 0.04482128564901319 0.6123923679137353 chr14 107349540 5115491 0.04765265878177028 0.6371779060148477 chr15 102531392 4761214 0.04643664644677798 0.6030478917800266 chr16 90354753 5326456 0.05895047934002985 0.7472756128221534 chr17 81195210 4611935 0.05680057973863237 0.7057663075479902 chr18 78077248 4676738 0.059898858115490956 0.9340048102017602 chr19 59128983 3091910 0.05229093826964688 0.7007396537711309 chr20 63025520 3560286 0.05648959342183928 0.6881658718884727 chr21 48129895 2401567 0.049897615608760416 0.6989774096917565 chr22 51304566 2008884 0.039156047046572814 0.5536594014724355 chrMT 16571 243559 14.697905980327077 14.79414199800665 chrX 155270560 4034578 0.02598417884240258 0.4586589980038043 chrY 59373566 1426171 0.02402030223348889 0.535857658625805