BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3212163.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 = 4,403,785 number of mapped reads = 3,890,188 (88.34%) number of supplementary alignments = 29,544 (0.67%) number of secondary alignments = 0 number of mapped bases = 262,027,526 bp number of sequenced bases = 261,907,225 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 185,663 duplication rate = 3.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7155 >>>>>>> ACTG content number of A's = 72,189,780 bp (27.56%) number of C's = 47,634,944 bp (18.19%) number of T's = 83,821,231 bp (32%) number of G's = 58,191,307 bp (22.22%) number of N's = 69,963 bp (0.03%) GC percentage = 40.41% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 2,248,214 number of insertions = 21,990 mapped reads with insertion percentage = 0.56% number of deletions = 70,335 mapped reads with deletion percentage = 1.79% homopolymer indels = 49.85% >>>>>>> Coverage mean coverageData = 0.0846X std coverageData = 0.7695X There is a 6.87% of reference with a coverageData >= 1X There is a 1.1% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.05% 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 0.01% 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% 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 26375356 0.10581861699754802 1.5805355325712716 chr2 243199373 16337457 0.06717721677678831 0.7638687163348523 chr3 198022430 16175247 0.08168391328194488 0.3526758112281724 chr4 191154276 11332176 0.059282879970731076 0.3561116256974227 chr5 180915260 18938003 0.10467885904152033 0.3851817286628875 chr6 171115067 18078277 0.10564982568133524 0.5340721283551818 chr7 159138663 17108588 0.10750742577245355 1.1829275132613688 chr8 146364022 15810124 0.10801919613824222 0.9688379814169469 chr9 141213431 9354808 0.06624587996874037 0.6740277024514163 chr10 135534747 8101974 0.05977783689668893 0.853448240913796 chr11 135006516 13761221 0.10193005054659732 0.8128220263448647 chr12 133851895 7397958 0.055269729278020305 0.297780959807429 chr13 115169878 8541851 0.07416740512653838 0.3155883232152224 chr14 107349540 9249983 0.08616695516347811 0.40284055037985306 chr15 102531392 8466794 0.08257757780173315 0.3369527797145349 chr16 90354753 8151667 0.09021846365957084 0.42552194220475076 chr17 81195210 4008558 0.04936939014013265 0.4028768836636434 chr18 78077248 8171539 0.10465966986951179 1.1786572643891184 chr19 59128983 6423478 0.1086350157586847 1.146141663198192 chr20 63025520 6005112 0.09528064187332369 0.38525096124549635 chr21 48129895 4008945 0.08329428102845435 0.4163447325689616 chr22 51304566 1673769 0.03262417228127415 0.2066220231861548 chrMT 16571 99411 5.99909480417597 3.652304076140848 chrX 155270560 17719011 0.11411700324903833 0.48200934940216733 chrY 59373566 736219 0.012399777368938898 0.2981568245816417