BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472481.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 14,217,418 number of mapped reads = 13,951,660 (98.13%) number of supplementary alignments = 47,586 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,013,797 number of mapped paired reads (second in pair) = 6,937,863 number of mapped paired reads (both in pair) = 13,825,536 number of mapped paired reads (singletons) = 126,124 number of mapped bases = 1,371,285,216 bp number of sequenced bases = 1,371,115,436 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,476,364 duplication rate = 45.27% >>>>>>> Insert size mean insert size = 26,566.3401 std insert size = 1,608,447.0685 median insert size = 229 >>>>>>> Mapping quality mean mapping quality = 54.9722 >>>>>>> ACTG content number of A's = 371,719,295 bp (27.11%) number of C's = 315,678,064 bp (23.02%) number of T's = 369,612,408 bp (26.96%) number of G's = 313,892,609 bp (22.89%) number of N's = 213,060 bp (0.02%) GC percentage = 45.92% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 8,062,330 number of insertions = 72,882 mapped reads with insertion percentage = 0.52% number of deletions = 67,289 mapped reads with deletion percentage = 0.48% homopolymer indels = 45.74% >>>>>>> Coverage mean coverageData = 0.443X std coverageData = 16.3721X There is a 4.55% of reference with a coverageData >= 1X There is a 2.01% of reference with a coverageData >= 2X There is a 0.86% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 158934560 0.6376496048930607 30.844125513326546 chr2 243199373 86630938 0.3562136568501762 11.469152588883663 chr3 198022430 156095139 0.788269990424822 18.84551988165701 chr4 191154276 54947422 0.2874506558252456 11.089490407763941 chr5 180915260 98140739 0.542467998553577 22.89819536045091 chr6 171115067 75549540 0.4415130784479662 13.583553045099734 chr7 159138663 63837496 0.40114385025341076 13.835789884478258 chr8 146364022 66149473 0.45195173032345337 15.243036378717235 chr9 141213431 83772868 0.5932358374608149 15.499504308926756 chr10 135534747 43557117 0.32137232675839206 13.461436055238396 chr11 135006516 84267164 0.6241710881569598 21.409135786531472 chr12 133851895 67718770 0.5059231324293167 13.664385244703436 chr13 115169878 33033694 0.2868258139511097 13.044018878168545 chr14 107349540 32451976 0.30230195676665217 13.135178962708073 chr15 102531392 27804146 0.2711769094093641 9.13823839432083 chr16 90354753 46307976 0.512512894590061 15.494515194697168 chr17 81195210 44459698 0.5475655275723778 13.858211220516436 chr18 78077248 23302753 0.29845766336436447 10.592094476999181 chr19 59128983 21498006 0.3635781457631362 10.439452556909597 chr20 63025520 29397079 0.46643135986819306 11.886114969534743 chr21 48129895 8512806 0.17687148496791857 8.751468721873978 chr22 51304566 14496198 0.28255181030086096 10.107808088599523 chrMT 16571 2216 0.13372759640335527 0.4594247784474466 chrX 155270560 48312644 0.31115134768625813 9.28691868271055 chrY 59373566 2104798 0.03545008564922646 1.3242815315844472