BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094073.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 423,956 number of mapped reads = 405,945 (95.75%) number of supplementary alignments = 12,800 (3.02%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 203,826 number of mapped paired reads (second in pair) = 202,119 number of mapped paired reads (both in pair) = 403,262 number of mapped paired reads (singletons) = 2,683 number of mapped bases = 53,765,113 bp number of sequenced bases = 52,587,957 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 386,571 duplication rate = 49.58% >>>>>>> Insert size mean insert size = 397,090.8068 std insert size = 5,638,341.2764 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 38.4788 >>>>>>> ACTG content number of A's = 14,001,329 bp (26.62%) number of C's = 12,339,481 bp (23.46%) number of T's = 13,342,895 bp (25.37%) number of G's = 12,903,755 bp (24.54%) number of N's = 497 bp (0%) GC percentage = 48% >>>>>>> Mismatches and indels general error rate = 0.0408 number of mismatches = 2,057,017 number of insertions = 34,491 mapped reads with insertion percentage = 8.32% number of deletions = 167,325 mapped reads with deletion percentage = 39.34% homopolymer indels = 26.75% >>>>>>> Coverage mean coverageData = 0.0174X std coverageData = 4.7952X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% 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 0.01% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 301091 0.001207984954228058 0.6382715134499023 chr2 243199373 2042807 0.008399721491058285 3.1131954603428746 chr3 198022430 1085080 0.005479581277737073 2.0268902264743702 chr4 191154276 819778 0.004288567418706344 1.433070828032852 chr5 180915260 516536 0.0028551267593457845 1.2959462023773964 chr6 171115067 1329082 0.007767182769475233 4.487359526529571 chr7 159138663 2110819 0.01326402371496611 5.058054307907748 chr8 146364022 881598 0.006023324502520162 2.128591431519543 chr9 141213431 620918 0.0043970180145258275 1.970445940460545 chr10 135534747 918712 0.0067784241335544755 2.4331083772603317 chr11 135006516 1494336 0.011068621310100321 3.7348809165694385 chr12 133851895 1324543 0.00989558646143934 2.940448825126947 chr13 115169878 1590521 0.01381021693884229 3.928482970910803 chr14 107349540 341912 0.0031850346075074005 1.4437600038651717 chr15 102531392 879938 0.008582132582380234 3.076989916924878 chr16 90354753 302846 0.0033517439862848167 1.2912853603427132 chr17 81195210 1101163 0.013561920709362043 4.918749370979478 chr18 78077248 150811 0.0019315614197877467 0.5722456717729612 chr19 59128983 251382 0.004251417616974742 1.0572705018688455 chr20 63025520 278435 0.004417813609471211 1.3716704635843353 chr21 48129895 685039 0.014233128910835979 6.130927138979773 chr22 51304566 95581 0.0018630115689897853 0.45716934615408505 chrMT 16571 1426222 86.06734656930783 397.82944778284656 chrX 155270560 32659832 0.2103414324003211 16.90404901962496 chrY 59373566 556131 0.00936664306132463 2.616851273087344