BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548941.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 = 10,235,713 number of mapped reads = 9,091,265 (88.82%) number of secondary alignments = 0 number of mapped bases = 358,938,807 bp number of sequenced bases = 358,901,265 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 412,334 duplication rate = 3.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 34.412 >>>>>>> ACTG content number of A's = 103,152,557 bp (28.74%) number of C's = 76,085,188 bp (21.2%) number of T's = 103,955,166 bp (28.96%) number of G's = 75,705,051 bp (21.09%) number of N's = 3,303 bp (0%) GC percentage = 42.29% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 1,274,531 number of insertions = 14,012 mapped reads with insertion percentage = 0.15% number of deletions = 29,154 mapped reads with deletion percentage = 0.32% homopolymer indels = 38.15% >>>>>>> Coverage mean coverageData = 0.1159X std coverageData = 1.0581X There is a 9.31% of reference with a coverageData >= 1X There is a 1.6% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% 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 29019103 0.11642539899629778 1.4384733274530388 chr2 243199373 30494920 0.12539061932532203 0.8726308635382566 chr3 198022430 24074904 0.12157665169546703 0.42276540344529945 chr4 191154276 22515539 0.11778726310051259 0.44565071585330623 chr5 180915260 21938068 0.12126156743217792 0.43898850062872263 chr6 171115067 21516864 0.12574499941609465 0.4660192637295165 chr7 159138663 20415180 0.12828548144833918 1.2038517348041256 chr8 146364022 17539575 0.11983528985012451 3.235349311289564 chr9 141213431 15196449 0.10761334026364673 0.8624047254372335 chr10 135534747 16942838 0.12500733852404652 0.7287493958503167 chr11 135006516 16446156 0.12181749805320508 0.7704704815063818 chr12 133851895 16797401 0.12549244073085405 0.4646824402237136 chr13 115169878 10780166 0.09360230458870504 0.35688277619924125 chr14 107349540 11193066 0.10426747986064962 0.5290175719167748 chr15 102531392 10332822 0.10077715515653976 0.38511104262906154 chr16 90354753 9974796 0.11039591907245876 0.49746071297943906 chr17 81195210 10113776 0.12456123951154262 0.4528093441297311 chr18 78077248 9087771 0.11639461216665833 1.72697001097977 chr19 59128983 7915735 0.13387233465524007 1.5531375746533627 chr20 63025520 7499690 0.1189944961977307 0.4614029972910607 chr21 48129895 4355978 0.09050462295835052 0.46073926333318604 chr22 51304566 4124172 0.0803860615446976 0.3829935673680682 chrMT 16571 6284 0.3792167038802728 0.7552045089043954 chrX 155270560 19223697 0.12380773921340917 0.6234896956534988 chrY 59373566 1433857 0.02414975378100079 0.26316364163946865