BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549157.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 = 14,267,025 number of mapped reads = 12,523,153 (87.78%) number of secondary alignments = 0 number of mapped bases = 497,123,294 bp number of sequenced bases = 497,076,756 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 767,541 duplication rate = 5.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4491 >>>>>>> ACTG content number of A's = 143,608,775 bp (28.89%) number of C's = 103,982,546 bp (20.92%) number of T's = 145,495,353 bp (29.27%) number of G's = 103,889,601 bp (20.9%) number of N's = 100,481 bp (0.02%) GC percentage = 41.82% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 1,516,392 number of insertions = 12,268 mapped reads with insertion percentage = 0.1% number of deletions = 37,102 mapped reads with deletion percentage = 0.3% homopolymer indels = 45.47% >>>>>>> Coverage mean coverageData = 0.1606X std coverageData = 0.8835X There is a 10.61% of reference with a coverageData >= 1X There is a 3.4% of reference with a coverageData >= 2X There is a 1.17% of reference with a coverageData >= 3X There is a 0.42% of reference with a coverageData >= 4X There is a 0.16% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 41422846 0.16618953980459691 1.642772117233783 chr2 243199373 41994357 0.17267461047278276 0.8163913896646992 chr3 198022430 34459624 0.17401879170960582 0.5845099475275127 chr4 191154276 31357885 0.16404490475536107 0.5899754172521684 chr5 180915260 30959975 0.1711297045920836 0.5881780425867602 chr6 171115067 29353065 0.1715399205611742 0.6266027209329779 chr7 159138663 27731628 0.17426078287461796 1.1040072517036437 chr8 146364022 26085134 0.1782209428489195 1.301580989328348 chr9 141213431 21607010 0.15300959580820608 0.7891384130947818 chr10 135534747 24119462 0.17795777491656808 0.8041825909890157 chr11 135006516 23466498 0.17381752151873914 0.7556374323194278 chr12 133851895 22883175 0.1709589169432379 0.6016664582081608 chr13 115169878 15568018 0.13517438995637385 0.5079481707228962 chr14 107349540 15497376 0.1443636926623067 0.6911872332573349 chr15 102531392 14937013 0.1456823389269893 0.5281533588689389 chr16 90354753 14256126 0.15777948062123529 0.6094944163892732 chr17 81195210 14017838 0.1726436571812549 0.6252465877513698 chr18 78077248 13305725 0.1704174435041563 1.4852083010848758 chr19 59128983 9904472 0.16750621264701948 1.32129981570291 chr20 63025520 10794430 0.17127078047114883 0.6121342390699217 chr21 48129895 6607312 0.13728083138348837 0.6051282306132802 chr22 51304566 6002485 0.11699709144796196 0.5084568865544429 chrMT 16571 154457 9.320922092812745 11.522981945888883 chrX 155270560 16709586 0.10761593182893138 0.5625210704629283 chrY 59373566 3927797 0.06615396824910263 0.5100863611798466