BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818971.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,911,341 number of mapped reads = 2,827,837 (97.13%) number of supplementary alignments = 42,479 (1.46%) number of secondary alignments = 0 number of mapped bases = 261,866,032 bp number of sequenced bases = 261,715,501 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,542,175 duplication rate = 45.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0814 >>>>>>> ACTG content number of A's = 75,439,188 bp (28.82%) number of C's = 55,945,302 bp (21.38%) number of T's = 76,936,417 bp (29.4%) number of G's = 53,381,324 bp (20.4%) number of N's = 13,270 bp (0.01%) GC percentage = 41.77% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,644,073 number of insertions = 39,612 mapped reads with insertion percentage = 1.36% number of deletions = 82,667 mapped reads with deletion percentage = 2.87% homopolymer indels = 42.27% >>>>>>> Coverage mean coverageData = 0.0846X std coverageData = 0.9688X There is a 3.12% of reference with a coverageData >= 1X There is a 1.77% of reference with a coverageData >= 2X There is a 1.13% of reference with a coverageData >= 3X There is a 0.74% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.32% of reference with a coverageData >= 6X There is a 0.22% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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% 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 25872262 0.10380019073252379 1.7954387920788095 chr2 243199373 20261973 0.08331424851165221 1.1357301057057263 chr3 198022430 13562895 0.06849171076226061 0.5593004603708346 chr4 191154276 14136832 0.07395509164545186 0.6678808524802459 chr5 180915260 14646652 0.08095863223478218 0.6178240731047364 chr6 171115067 11450989 0.0669198171777591 0.6768111178865973 chr7 159138663 13161517 0.08270471016838944 1.267487734820823 chr8 146364022 25046254 0.1711230236621948 1.0004260371926748 chr9 141213431 11285765 0.0799199121505659 0.9291253782546397 chr10 135534747 13903628 0.10258349469601327 1.1175280515281665 chr11 135006516 9068052 0.06716751360356563 0.6757315506570923 chr12 133851895 12209712 0.09121807352820817 0.6693607281453781 chr13 115169878 5889686 0.05113911816421304 0.48366603367334055 chr14 107349540 5881978 0.05479276390005956 0.5134283661661521 chr15 102531392 6879792 0.06709937186847127 0.5562254625861938 chr16 90354753 8482144 0.09387601336257319 0.923379041863678 chr17 81195210 8064696 0.09932477543933935 0.7820785159021324 chr18 78077248 6145617 0.07871200839455816 1.1016127245444773 chr19 59128983 5467477 0.09246695482653575 1.6321250732654304 chr20 63025520 7531304 0.11949610253116516 0.822818358348282 chr21 48129895 3387554 0.07038357345263271 0.631659968218771 chr22 51304566 1946696 0.037943913218172434 0.4555007814685651 chrMT 16571 63649 3.8409872669120753 4.885325116892847 chrX 155270560 16576532 0.10675901471598995 0.8059401473659606 chrY 59373566 942376 0.01587197912283052 0.7822001627214807