BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083752.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 = 1,755,848 number of mapped reads = 1,418,479 (80.79%) number of supplementary alignments = 9,575 (0.55%) number of secondary alignments = 0 number of mapped bases = 93,837,704 bp number of sequenced bases = 93,808,600 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,490 duplication rate = 1.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.061 >>>>>>> ACTG content number of A's = 27,960,341 bp (29.81%) number of C's = 17,387,503 bp (18.54%) number of T's = 27,123,793 bp (28.91%) number of G's = 21,323,792 bp (22.73%) number of N's = 13,171 bp (0.01%) GC percentage = 41.27% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 829,724 number of insertions = 6,647 mapped reads with insertion percentage = 0.46% number of deletions = 17,818 mapped reads with deletion percentage = 1.25% homopolymer indels = 46.11% >>>>>>> Coverage mean coverageData = 0.0303X std coverageData = 0.2583X There is a 2.78% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 9434994 0.03785344229894617 0.5250338284449785 chr2 243199373 8172142 0.03360264419760654 0.24274594688216908 chr3 198022430 7827542 0.03952856249668282 0.2126761898046603 chr4 191154276 4365481 0.02283747500369806 0.16209077646818354 chr5 180915260 4494519 0.02484322770782299 0.16724952677750923 chr6 171115067 6302787 0.03683361793032521 0.23359123338351218 chr7 159138663 6617890 0.041585683046740186 0.3564810882338704 chr8 146364022 6399486 0.04372308107247832 0.29712417103951066 chr9 141213431 3714577 0.026304700436037137 0.19631371905571812 chr10 135534747 4218325 0.03112356862996911 0.23770072669139614 chr11 135006516 3561901 0.026383178423773263 0.1985227213023849 chr12 133851895 3320446 0.024806865827338494 0.16733840341889422 chr13 115169878 2839205 0.02465232271931381 0.16541452735805995 chr14 107349540 2022634 0.0188415711888472 0.1485797554505854 chr15 102531392 2394522 0.023354037756553623 0.16250361522237436 chr16 90354753 2622263 0.029021860089640222 0.18916550889381528 chr17 81195210 1986593 0.02446687433901581 0.17057791487287424 chr18 78077248 2436330 0.031204096742754046 0.3384747217688845 chr19 59128983 2621050 0.04432766922441402 0.3377595267539191 chr20 63025520 2071338 0.03286506799150566 0.194006340388696 chr21 48129895 1481961 0.03079086293456489 0.18962103899855443 chr22 51304566 739710 0.014418014957966898 0.12679210408209607 chrMT 16571 4667 0.2816365940498461 0.5561647291575926 chrX 155270560 3998305 0.025750567267870998 0.17594680950616687 chrY 59373566 189036 0.0031838411053161267 0.08212201298007125