BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549150.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 14,842,191 number of mapped reads = 12,859,967 (86.64%) number of secondary alignments = 0 number of mapped bases = 510,672,649 bp number of sequenced bases = 510,613,858 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 734,281 duplication rate = 4.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0336 >>>>>>> ACTG content number of A's = 149,648,691 bp (29.31%) number of C's = 104,822,558 bp (20.53%) number of T's = 151,160,062 bp (29.6%) number of G's = 104,878,828 bp (20.54%) number of N's = 103,719 bp (0.02%) GC percentage = 41.07% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 1,624,866 number of insertions = 12,379 mapped reads with insertion percentage = 0.1% number of deletions = 44,869 mapped reads with deletion percentage = 0.35% homopolymer indels = 45.17% >>>>>>> Coverage mean coverageData = 0.165X std coverageData = 1.1753X There is a 11.58% of reference with a coverageData >= 1X There is a 3.23% of reference with a coverageData >= 2X There is a 0.95% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 41623661 0.16699521482837149 2.044495600588677 chr2 243199373 44255852 0.18197354480843994 0.8793976517377725 chr3 198022430 35367387 0.17860293402116115 0.5595735371683088 chr4 191154276 34246001 0.17915372711829894 0.6493395948296492 chr5 180915260 32224538 0.1781195129697738 0.5744802619262579 chr6 171115067 30398609 0.17765010137885753 0.6457595173835852 chr7 159138663 28586526 0.17963281493699618 1.3832970667038713 chr8 146364022 26671001 0.1822237503148144 3.1413023250009786 chr9 141213431 21679804 0.15352508501829404 0.7989098411838366 chr10 135534747 24334482 0.1795442315615198 0.9352529838882179 chr11 135006516 23726878 0.17574616917008656 0.7997111935290464 chr12 133851895 23666003 0.17680738102363064 0.5847236412651776 chr13 115169878 16747492 0.14541555735606493 0.4970339088080597 chr14 107349540 15853006 0.14767651542801208 0.6802364480895674 chr15 102531392 15036914 0.1466566844230497 0.5001716947159289 chr16 90354753 14453763 0.15996682543086582 0.6084866214519107 chr17 81195210 13248569 0.16316934213237455 0.5891969807128689 chr18 78077248 13971270 0.1789416297049814 1.679380485841305 chr19 59128983 9693597 0.16393985670276115 1.6124860085276393 chr20 63025520 10726567 0.17019402616590867 0.603347487990654 chr21 48129895 6606808 0.13727035972133328 0.6266334737963898 chr22 51304566 5889962 0.114803855859535 0.4858726504004771 chrMT 16571 146397 8.83453020336733 10.845757758617337 chrX 155270560 17043561 0.10976685470832333 0.5814721648533558 chrY 59373566 4474001 0.07535341569344176 0.7365309679609098