BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472670.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 19,702,462 number of mapped reads = 19,569,395 (99.32%) number of supplementary alignments = 103,962 (0.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,808,609 number of mapped paired reads (second in pair) = 9,760,786 number of mapped paired reads (both in pair) = 19,488,194 number of mapped paired reads (singletons) = 81,201 number of mapped bases = 1,922,683,470 bp number of sequenced bases = 1,922,413,436 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,145,339 duplication rate = 50.24% >>>>>>> Insert size mean insert size = 19,234.6587 std insert size = 1,358,092.812 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 54.7854 >>>>>>> ACTG content number of A's = 508,590,848 bp (26.46%) number of C's = 455,188,231 bp (23.68%) number of T's = 509,961,673 bp (26.53%) number of G's = 448,307,873 bp (23.32%) number of N's = 364,811 bp (0.02%) GC percentage = 47% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 10,705,472 number of insertions = 110,599 mapped reads with insertion percentage = 0.56% number of deletions = 108,982 mapped reads with deletion percentage = 0.54% homopolymer indels = 46.48% >>>>>>> Coverage mean coverageData = 0.6211X std coverageData = 28.9603X There is a 3.75% of reference with a coverageData >= 1X There is a 1.83% of reference with a coverageData >= 2X There is a 0.86% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 210919765 0.8462156048148823 35.75447551121152 chr2 243199373 146955534 0.6042595101591812 27.66836206282308 chr3 198022430 201631685 1.0182264958570602 37.286743500297554 chr4 191154276 35961632 0.18812883892798715 9.226250361407532 chr5 180915260 57417253 0.3173709779926801 14.554883493611031 chr6 171115067 144652625 0.8453529401943314 26.56865268367554 chr7 159138663 87477844 0.5496957329596265 23.635183570656643 chr8 146364022 94616173 0.6464441992445384 27.355344892003174 chr9 141213431 124147403 0.8791472745959978 28.58148786699379 chr10 135534747 36076012 0.266175374201274 12.893230541057628 chr11 135006516 41260028 0.30561508601555204 14.8060671997456 chr12 133851895 67035913 0.5008215460827058 17.275041733306697 chr13 115169878 82374302 0.7152417231873772 50.607112611765075 chr14 107349540 22581729 0.210357016900119 12.070728292348168 chr15 102531392 15136212 0.1476251487934544 6.963960870199427 chr16 90354753 132527457 1.466745827969891 63.22724605937791 chr17 81195210 93305348 1.1491484288297302 43.29856484589926 chr18 78077248 9898340 0.1267762408839 6.600596997523217 chr19 59128983 75088879 1.2699166329310958 42.159357144868665 chr20 63025520 86635325 1.3746070639321977 38.59698897424358 chr21 48129895 14607081 0.30349289147628516 18.51448419649318 chr22 51304566 20877161 0.40692598393679036 15.67437853159718 chrMT 16571 6443 0.38881177961499 0.8922346421686471 chrX 155270560 120127263 0.7736641318225426 33.47827444738765 chrY 59373566 1366063 0.023007932520003934 1.0768822593053036