BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549066.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 = 9,592,533 number of mapped reads = 8,256,776 (86.08%) number of secondary alignments = 0 number of mapped bases = 328,167,100 bp number of sequenced bases = 328,131,444 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 355,703 duplication rate = 3.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4975 >>>>>>> ACTG content number of A's = 96,683,075 bp (29.46%) number of C's = 67,385,234 bp (20.54%) number of T's = 96,804,620 bp (29.5%) number of G's = 67,252,261 bp (20.5%) number of N's = 6,254 bp (0%) GC percentage = 41.03% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 1,009,172 number of insertions = 7,821 mapped reads with insertion percentage = 0.09% number of deletions = 27,726 mapped reads with deletion percentage = 0.34% homopolymer indels = 44.79% >>>>>>> Coverage mean coverageData = 0.106X std coverageData = 1.0234X There is a 8.3% of reference with a coverageData >= 1X There is a 1.65% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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% 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 26948937 0.10811983894716154 1.9974101990637276 chr2 243199373 28200162 0.11595491243310072 0.5840024372979655 chr3 198022430 22819367 0.11523627399178972 0.41058115799155054 chr4 191154276 22355248 0.11694872051933591 0.47790070488902414 chr5 180915260 20863372 0.11532123934708438 0.4173120317702309 chr6 171115067 19496462 0.11393772823055962 0.47308206789840485 chr7 159138663 18212667 0.11444526840092907 0.7890277809846185 chr8 146364022 17372040 0.11869064379769503 3.0849118383324052 chr9 141213431 14161313 0.1002830460227257 0.5489978728282733 chr10 135534747 15695108 0.11580135977971759 0.6758653710524197 chr11 135006516 15347998 0.11368338695593033 0.5605210274354222 chr12 133851895 15088269 0.1127236114214147 0.4227690510804368 chr13 115169878 10866927 0.0943556352469176 0.3658180438485688 chr14 107349540 10291223 0.09586648438363127 0.41349761563064075 chr15 102531392 9257114 0.09028565612373624 0.3588174352302635 chr16 90354753 9031925 0.09996070710303419 0.43383735728913897 chr17 81195210 8438845 0.10393279357242872 0.4241029116636501 chr18 78077248 8931167 0.11438885499652857 1.0417318401758247 chr19 59128983 6084224 0.10289749106626779 1.3978991974866661 chr20 63025520 6825188 0.10829245042325712 0.4183809152318009 chr21 48129895 4385254 0.09111289355607362 0.4526431054708548 chr22 51304566 3664896 0.07143410978274331 0.3534051331028561 chrMT 16571 4050 0.2444028724880816 0.579046365610075 chrX 155270560 10676423 0.06876012426309276 0.39125993146767796 chrY 59373566 3148921 0.0530357398442263 0.6408890771850638