BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716416.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,019,488 number of mapped reads = 922,847 (90.52%) number of supplementary alignments = 5,225 (0.51%) number of secondary alignments = 0 number of mapped bases = 53,596,746 bp number of sequenced bases = 53,581,851 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,580 duplication rate = 2.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2923 >>>>>>> ACTG content number of A's = 13,230,110 bp (24.69%) number of C's = 10,715,769 bp (20%) number of T's = 16,534,480 bp (30.86%) number of G's = 13,100,763 bp (24.45%) number of N's = 729 bp (0%) GC percentage = 44.45% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 262,350 number of insertions = 3,346 mapped reads with insertion percentage = 0.36% number of deletions = 9,519 mapped reads with deletion percentage = 1.02% homopolymer indels = 42.81% >>>>>>> Coverage mean coverageData = 0.0173X std coverageData = 0.1796X There is a 1.6% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 6467484 0.02594771468994655 0.304985955731597 chr2 243199373 4637216 0.019067549158525175 0.22206878888611387 chr3 198022430 3766150 0.01901880509192822 0.1476846810904289 chr4 191154276 2496573 0.013060513488068663 0.12505940376624747 chr5 180915260 2386088 0.013188981404885359 0.12210413007715464 chr6 171115067 4058156 0.02371594781890247 0.18948817854725128 chr7 159138663 3110550 0.01954616145040756 0.21841786033477917 chr8 146364022 4123927 0.028175824520591544 0.19060021968030663 chr9 141213431 2275170 0.01611156944412745 0.1686711184030722 chr10 135534747 2768364 0.020425492807390564 0.19345474843391516 chr11 135006516 1797768 0.0133161572734756 0.14359169016123052 chr12 133851895 2401206 0.017939275346083073 0.14432688843982783 chr13 115169878 1211677 0.010520780442261127 0.108977881256371 chr14 107349540 1184017 0.011029548892338058 0.12131613327251316 chr15 102531392 1606697 0.015670293445347937 0.13498633957950087 chr16 90354753 1187001 0.013137117424248838 0.1311538699324922 chr17 81195210 1312628 0.016166323111917562 0.13657531675560025 chr18 78077248 1048211 0.013425306691137475 0.2432346114189943 chr19 59128983 1233799 0.02086623069434494 0.21175710845007042 chr20 63025520 936533 0.01485958386380628 0.1296572636144454 chr21 48129895 501411 0.010417870223901381 0.11574352505482467 chr22 51304566 684743 0.013346628836115678 0.12259236453585491 chrMT 16571 18091 1.0917265101683664 1.2870953798301754 chrX 155270560 2267227 0.014601782849240706 0.13951977209513317 chrY 59373566 116059 0.0019547251044345223 0.0562818353567393