BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006222.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 7,197,444 number of mapped reads = 1,492,562 (20.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 752,874 number of mapped paired reads (second in pair) = 739,688 number of mapped paired reads (both in pair) = 1,331,564 number of mapped paired reads (singletons) = 160,998 number of mapped bases = 57,678,936 bp number of sequenced bases = 57,670,790 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,876 duplication rate = 2.75% >>>>>>> Insert size mean insert size = 69,074.7717 std insert size = 2,487,013.7692 median insert size = 129 >>>>>>> Mapping quality mean mapping quality = 47.6167 >>>>>>> ACTG content number of A's = 16,131,740 bp (27.97%) number of C's = 12,409,828 bp (21.52%) number of T's = 16,431,779 bp (28.49%) number of G's = 12,695,001 bp (22.01%) number of N's = 2,442 bp (0%) GC percentage = 43.53% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 228,386 number of insertions = 1,946 mapped reads with insertion percentage = 0.13% number of deletions = 6,052 mapped reads with deletion percentage = 0.4% homopolymer indels = 42.02% >>>>>>> Coverage mean coverageData = 0.0186X std coverageData = 0.2996X There is a 1.69% of reference with a coverageData >= 1X There is a 0.14% 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 4904053 0.019675188692910017 0.2503920219100103 chr2 243199373 4764043 0.01958904310168596 0.5029152141170037 chr3 198022430 3901913 0.01970439914306677 0.1512867933177137 chr4 191154276 3652700 0.019108649183448033 0.1527521882602465 chr5 180915260 3582318 0.019801082562079065 0.7236293610649426 chr6 171115067 3160919 0.018472476184695063 0.2544867616035605 chr7 159138663 2914537 0.018314449455943967 0.16274296162774102 chr8 146364022 2946306 0.02012998795564664 0.23176932453659221 chr9 141213431 2315381 0.016396322811532 0.1440717479237524 chr10 135534747 2771053 0.020445332738179677 0.17450148321127124 chr11 135006516 2576162 0.019081760468509536 0.18663868900738395 chr12 133851895 2579854 0.019273944533994083 0.15023868887027308 chr13 115169878 1897669 0.01647712954944695 0.1599553166730984 chr14 107349540 1895443 0.017656740774110443 0.17440525585931066 chr15 102531392 1665623 0.016245005237030236 0.1368652069113633 chr16 90354753 1818366 0.02012474097516486 0.1608519262175832 chr17 81195210 1715224 0.02112469442470806 0.6613066451040782 chr18 78077248 1530521 0.019602650441777867 0.19992927088974377 chr19 59128983 1220716 0.02064496864422647 0.1780700126314183 chr20 63025520 1241465 0.019697814472613633 0.15343428878848375 chr21 48129895 730771 0.015183307588765776 0.1864140389149394 chr22 51304566 691371 0.01347581811724126 0.12589239114082698 chrMT 16571 429 0.02588860056725605 0.15880296259177634 chrX 155270560 3057547 0.01969173679801245 0.15584078080310476 chrY 59373566 144552 0.002434618799888152 0.0742691643090498