BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926997.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 28,765,196 number of mapped reads = 28,054,925 (97.53%) number of supplementary alignments = 724,802 (2.52%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,043,236 number of mapped paired reads (second in pair) = 14,011,689 number of mapped paired reads (both in pair) = 27,636,240 number of mapped paired reads (singletons) = 418,685 number of mapped bases = 2,553,642,143 bp number of sequenced bases = 2,551,639,629 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,042,224 duplication rate = 8.34% >>>>>>> Insert size mean insert size = 244,383.2789 std insert size = 4,790,914.1767 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 53.0856 >>>>>>> ACTG content number of A's = 741,706,603 bp (29.07%) number of C's = 480,173,756 bp (18.82%) number of T's = 760,025,066 bp (29.79%) number of G's = 569,254,409 bp (22.31%) number of N's = 479,795 bp (0.02%) GC percentage = 41.13% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 24,716,678 number of insertions = 442,029 mapped reads with insertion percentage = 1.55% number of deletions = 1,411,783 mapped reads with deletion percentage = 4.9% homopolymer indels = 52.71% >>>>>>> Coverage mean coverageData = 0.8249X std coverageData = 3.4992X There is a 31.65% of reference with a coverageData >= 1X There is a 17.98% of reference with a coverageData >= 2X There is a 10.65% of reference with a coverageData >= 3X There is a 6.69% of reference with a coverageData >= 4X There is a 4.33% of reference with a coverageData >= 5X There is a 2.88% of reference with a coverageData >= 6X There is a 1.95% of reference with a coverageData >= 7X There is a 1.35% of reference with a coverageData >= 8X There is a 0.95% of reference with a coverageData >= 9X There is a 0.68% of reference with a coverageData >= 10X There is a 0.49% of reference with a coverageData >= 11X There is a 0.36% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 206511923 0.8285312276112644 3.7006971087998513 chr2 243199373 219437547 0.9022948714592286 4.340704733990252 chr3 198022430 175102873 0.8842577732229626 1.8502514394750154 chr4 191154276 162699418 0.8511419226635558 2.474152338368037 chr5 180915260 159443587 0.8813164074716527 1.8348980865416817 chr6 171115067 150185624 0.877687901089388 2.300011098820522 chr7 159138663 132161903 0.830482677864398 2.5739631766402065 chr8 146364022 127340889 0.8700286262972468 2.098636930892902 chr9 141213431 106020077 0.7507789892874992 3.591915711336488 chr10 135534747 127720972 0.9423485477122704 6.0810996289511365 chr11 135006516 119435327 0.8846634261712227 2.7723182401203594 chr12 133851895 114107545 0.8524910685799405 1.833859610109902 chr13 115169878 80693562 0.700648150378348 1.6393368781428737 chr14 107349540 77613602 0.7229989248207305 1.7274410946530292 chr15 102531392 74313915 0.7247918276580113 1.7380092739296298 chr16 90354753 73041931 0.8083905779699271 3.5032238068502 chr17 81195210 59050835 0.7272699337805765 2.0833016013027836 chr18 78077248 67700739 0.8670994525831648 3.39879126330615 chr19 59128983 35808627 0.6056019431282963 2.352340422048072 chr20 63025520 57861852 0.9180702039427838 1.9884108250012267 chr21 48129895 33042262 0.686522627984125 2.58146766244539 chr22 51304566 27715720 0.5402193637112144 1.5189027477762538 chrMT 16571 10385529 626.7291654094503 524.5804491168187 chrX 155270560 151838367 0.9778954039967396 2.267554111024622 chrY 59373566 4407517 0.07423365812321261 2.28443803953689