BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3212679.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,737,889 number of mapped reads = 2,566,653 (93.75%) number of supplementary alignments = 15,122 (0.55%) number of secondary alignments = 0 number of mapped bases = 176,330,567 bp number of sequenced bases = 176,265,468 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 117,776 duplication rate = 3.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5615 >>>>>>> ACTG content number of A's = 50,100,217 bp (28.42%) number of C's = 33,356,985 bp (18.92%) number of T's = 55,315,088 bp (31.38%) number of G's = 37,491,166 bp (21.27%) number of N's = 2,012 bp (0%) GC percentage = 40.19% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,440,513 number of insertions = 12,574 mapped reads with insertion percentage = 0.49% number of deletions = 36,939 mapped reads with deletion percentage = 1.42% homopolymer indels = 48.99% >>>>>>> Coverage mean coverageData = 0.057X std coverageData = 0.3847X There is a 4.45% of reference with a coverageData >= 1X There is a 0.88% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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% 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 14077308 0.056478527289205833 0.5376831728395599 chr2 243199373 14998396 0.0616711951802606 0.4209759443310943 chr3 198022430 12377892 0.06250752503138154 0.3065474922442491 chr4 191154276 11813985 0.06180340428272711 0.3210287744547249 chr5 180915260 11236412 0.062108702162548365 0.30851322597633035 chr6 171115067 10295481 0.060167004463727324 0.3661750557671235 chr7 159138663 9267509 0.0582354333340101 0.49242067893875396 chr8 146364022 8796511 0.06010022736325188 0.4538305464969542 chr9 141213431 7423362 0.05256838494349734 0.3799735544625833 chr10 135534747 8200412 0.060504130354115025 0.3622123183188703 chr11 135006516 8118842 0.060136667773872485 0.3777055363148656 chr12 133851895 7945543 0.05936070609982772 0.3017440157970759 chr13 115169878 5879015 0.05104646372899692 0.2793794317672798 chr14 107349540 5416323 0.050455018251591946 0.2967806547670668 chr15 102531392 4804303 0.04685689822683769 0.2727380239031196 chr16 90354753 4705097 0.05207359705803191 0.3018764410793608 chr17 81195210 3921853 0.048301531580495945 0.3111835112370255 chr18 78077248 4848025 0.06209267263108454 0.6999686592373002 chr19 59128983 2940161 0.049724531876355796 0.42740240702744986 chr20 63025520 3580295 0.056807067994044315 0.3009212611712899 chr21 48129895 2406654 0.05000330875436151 0.2971597531436219 chr22 51304566 1810429 0.03528787281818153 0.2277262154951655 chrMT 16571 93536 5.64455977309758 4.1004691537517655 chrX 155270560 10959482 0.07058312921651085 0.3583570087234425 chrY 59373566 413741 0.006968437772459212 0.14715177827899042