BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080800.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 = 3,431,216 number of mapped reads = 2,816,911 (82.1%) number of supplementary alignments = 33,419 (0.97%) number of secondary alignments = 0 number of mapped bases = 198,825,048 bp number of sequenced bases = 198,750,820 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 182,543 duplication rate = 5.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.872 >>>>>>> ACTG content number of A's = 60,936,328 bp (30.66%) number of C's = 36,628,051 bp (18.43%) number of T's = 61,659,707 bp (31.02%) number of G's = 39,498,517 bp (19.87%) number of N's = 28,217 bp (0.01%) GC percentage = 38.3% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,601,156 number of insertions = 15,525 mapped reads with insertion percentage = 0.55% number of deletions = 41,358 mapped reads with deletion percentage = 1.45% homopolymer indels = 47.27% >>>>>>> Coverage mean coverageData = 0.0642X std coverageData = 0.6986X There is a 3.6% of reference with a coverageData >= 1X There is a 1.5% of reference with a coverageData >= 2X There is a 0.67% of reference with a coverageData >= 3X There is a 0.31% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 14525514 0.05827674146496911 0.697267041787674 chr2 243199373 18857606 0.07753969826229774 0.5592503732126982 chr3 198022430 14033213 0.070866785141461 0.4254246546314092 chr4 191154276 13329326 0.06973072367996623 0.4338196568707558 chr5 180915260 12055579 0.06663660655270318 0.4117574640238142 chr6 171115067 12180141 0.0711809965863497 0.46583359341328195 chr7 159138663 12269247 0.07709783888281127 0.5796902090605623 chr8 146364022 9918393 0.06776523946574795 2.3858373552617214 chr9 141213431 7738971 0.05480336356957434 0.45071734185961465 chr10 135534747 9028629 0.06661486592807082 0.4809571175972042 chr11 135006516 8791593 0.06511976799697579 0.42878901418505877 chr12 133851895 8981780 0.06710237460590304 0.4158618551478914 chr13 115169878 7313715 0.06350371405273174 0.40745919495527083 chr14 107349540 5864747 0.054632250869449464 0.37907090042788516 chr15 102531392 4313021 0.042065370574506586 0.32042413533551845 chr16 90354753 5523319 0.06112925791518682 0.3996936262371109 chr17 81195210 4047316 0.04984673356962806 0.3517895031100942 chr18 78077248 5261989 0.06739465253693368 0.6618295890494412 chr19 59128983 3135853 0.053034110192627534 0.5437944922118003 chr20 63025520 3604922 0.057197814472613635 0.38127739144524736 chr21 48129895 2290383 0.04758753369397544 0.3575909802134025 chr22 51304566 1891832 0.036874534714902374 0.2937975128479086 chrMT 16571 19075 1.15110735622473 1.6311739160433771 chrX 155270560 13366270 0.08608373667229641 0.48038341253637973 chrY 59373566 482614 0.00812843210394336 0.17645703397979934