BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818938.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 = 227,134 number of mapped reads = 221,622 (97.57%) number of supplementary alignments = 3,011 (1.33%) number of secondary alignments = 0 number of mapped bases = 20,530,547 bp number of sequenced bases = 20,519,599 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,576 duplication rate = 9.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1466 >>>>>>> ACTG content number of A's = 5,895,688 bp (28.73%) number of C's = 4,534,271 bp (22.1%) number of T's = 5,765,299 bp (28.1%) number of G's = 4,323,356 bp (21.07%) number of N's = 985 bp (0%) GC percentage = 43.17% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 128,553 number of insertions = 2,625 mapped reads with insertion percentage = 1.15% number of deletions = 6,123 mapped reads with deletion percentage = 2.72% homopolymer indels = 43.23% >>>>>>> Coverage mean coverageData = 0.0066X std coverageData = 0.107X There is a 0.57% of reference with a coverageData >= 1X There is a 0.07% 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 2462013 0.009877660445227136 0.15311986161895755 chr2 243199373 1775289 0.007299726878818886 0.142776379933396 chr3 198022430 1324582 0.006689050326268595 0.09212014092264652 chr4 191154276 1270555 0.0066467516530993006 0.09345172307899062 chr5 180915260 1028347 0.005684136318848947 0.0857808155480316 chr6 171115067 1104694 0.006455854644290325 0.09259846223770299 chr7 159138663 1049871 0.0065972088756331955 0.0964227611806929 chr8 146364022 1322954 0.009038792333815479 0.11055697882150554 chr9 141213431 754520 0.005343117822836555 0.10105398128125734 chr10 135534747 988891 0.007296217552241419 0.11509782924271585 chr11 135006516 803301 0.005950090586738791 0.09022424898283635 chr12 133851895 920414 0.006876361369407583 0.09368822556228272 chr13 115169878 306989 0.0026655320412860037 0.05785077569331792 chr14 107349540 660281 0.006150757609208199 0.09067423185378047 chr15 102531392 567528 0.005535163318566864 0.08416880854157474 chr16 90354753 638856 0.007070530091538184 0.12322108161056866 chr17 81195210 476478 0.005868301837017233 0.08817937265345334 chr18 78077248 531144 0.006802801246273435 0.12835051283384685 chr19 59128983 360696 0.006100155654630488 0.14287959774304063 chr20 63025520 439796 0.006978062219875378 0.09657170845695887 chr21 48129895 262221 0.005448193892797813 0.08454393065866929 chr22 51304566 257921 0.005027252350209921 0.08327738546121288 chrMT 16571 566 0.03415605576006276 0.23570950092742948 chrX 155270560 1166344 0.007511687985153142 0.1035061078499379 chrY 59373566 56296 9.481660576021322E-4 0.06760759146837461