BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173851.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 = 1,394,898 number of mapped reads = 1,359,232 (97.44%) number of supplementary alignments = 127,668 (9.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 679,512 number of mapped paired reads (second in pair) = 679,720 number of mapped paired reads (both in pair) = 1,337,020 number of mapped paired reads (singletons) = 22,212 number of mapped bases = 160,703,789 bp number of sequenced bases = 160,617,356 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,030,378 duplication rate = 63.96% >>>>>>> Insert size mean insert size = 820,616.8472 std insert size = 8,578,228.4342 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 52.9887 >>>>>>> ACTG content number of A's = 48,542,048 bp (30.22%) number of C's = 31,381,322 bp (19.54%) number of T's = 48,306,021 bp (30.08%) number of G's = 32,385,935 bp (20.16%) number of N's = 2,030 bp (0%) GC percentage = 39.7% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 1,642,145 number of insertions = 18,439 mapped reads with insertion percentage = 1.3% number of deletions = 33,398 mapped reads with deletion percentage = 2.4% homopolymer indels = 43.1% >>>>>>> Coverage mean coverageData = 0.0519X std coverageData = 0.935X There is a 1.16% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.68% of reference with a coverageData >= 3X There is a 0.55% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.33% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.19% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% 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 0.01% 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% 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 13006849 0.052183817828883164 0.7531699403198909 chr2 243199373 15028581 0.061795311454195236 2.328469918501887 chr3 198022430 11267270 0.05689895836547405 0.667976972479688 chr4 191154276 10462447 0.05473300006116526 0.7277598568943604 chr5 180915260 11843990 0.06546705899767659 0.7182852794540355 chr6 171115067 9331689 0.054534584029353766 0.6924169743893521 chr7 159138663 7938886 0.049886594811972246 0.705994158971966 chr8 146364022 7888563 0.053896872279172545 0.8822902629757596 chr9 141213431 6246502 0.04423447511873003 0.654894614504474 chr10 135534747 9295506 0.06858393294525425 0.9087781073524729 chr11 135006516 7023677 0.052024725976929885 0.6455482640663613 chr12 133851895 7041306 0.052605202190077326 0.6416822051341062 chr13 115169878 4752702 0.041266884037161174 0.5721491650923152 chr14 107349540 5053968 0.04707954966551324 0.607138629932117 chr15 102531392 4272513 0.04167029157275071 0.5601681175646172 chr16 90354753 4837733 0.053541544184178114 0.6846858391894155 chr17 81195210 4260360 0.05247058293217051 0.6404165778189409 chr18 78077248 4531675 0.05804091609376396 0.9357285939439733 chr19 59128983 3029231 0.05123089974336274 0.6994296940202516 chr20 63025520 3334108 0.05290092013520872 0.6489517836934171 chr21 48129895 2218850 0.0461012848667133 0.6808877504158772 chr22 51304566 2212322 0.043121347133118715 0.5996093525633918 chrMT 16571 247626 14.943334741415727 15.144857835395541 chrX 155270560 4195690 0.027021799882733726 0.4581732119509673 chrY 59373566 1381745 0.023272056793759027 0.488967520011901