BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472705.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 = 18,187,568 number of mapped reads = 18,051,414 (99.25%) number of supplementary alignments = 114,879 (0.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,048,475 number of mapped paired reads (second in pair) = 9,002,939 number of mapped paired reads (both in pair) = 17,968,256 number of mapped paired reads (singletons) = 83,158 number of mapped bases = 1,776,924,016 bp number of sequenced bases = 1,776,676,658 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,746,612 duplication rate = 44.06% >>>>>>> Insert size mean insert size = 23,496.7262 std insert size = 1,475,741.1555 median insert size = 221 >>>>>>> Mapping quality mean mapping quality = 54.923 >>>>>>> ACTG content number of A's = 477,776,048 bp (26.89%) number of C's = 412,880,390 bp (23.24%) number of T's = 476,323,002 bp (26.81%) number of G's = 409,349,102 bp (23.04%) number of N's = 348,116 bp (0.02%) GC percentage = 46.28% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 10,208,809 number of insertions = 108,864 mapped reads with insertion percentage = 0.6% number of deletions = 106,618 mapped reads with deletion percentage = 0.57% homopolymer indels = 43.94% >>>>>>> Coverage mean coverageData = 0.574X std coverageData = 42.9811X There is a 3.55% of reference with a coverageData >= 1X There is a 1.89% of reference with a coverageData >= 2X There is a 1.03% of reference with a coverageData >= 3X There is a 0.74% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.29% of reference with a coverageData >= 9X There is a 0.26% of reference with a coverageData >= 10X There is a 0.24% of reference with a coverageData >= 11X There is a 0.23% of reference with a coverageData >= 12X There is a 0.21% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.19% of reference with a coverageData >= 15X There is a 0.18% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.17% of reference with a coverageData >= 18X There is a 0.16% of reference with a coverageData >= 19X There is a 0.16% of reference with a coverageData >= 20X There is a 0.15% of reference with a coverageData >= 21X There is a 0.15% of reference with a coverageData >= 22X There is a 0.14% of reference with a coverageData >= 23X There is a 0.14% of reference with a coverageData >= 24X There is a 0.13% of reference with a coverageData >= 25X There is a 0.13% of reference with a coverageData >= 26X There is a 0.13% of reference with a coverageData >= 27X There is a 0.12% of reference with a coverageData >= 28X There is a 0.12% of reference with a coverageData >= 29X There is a 0.12% of reference with a coverageData >= 30X There is a 0.12% of reference with a coverageData >= 31X There is a 0.12% of reference with a coverageData >= 32X There is a 0.11% of reference with a coverageData >= 33X There is a 0.11% of reference with a coverageData >= 34X There is a 0.11% of reference with a coverageData >= 35X There is a 0.11% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.1% of reference with a coverageData >= 38X There is a 0.1% of reference with a coverageData >= 39X There is a 0.1% of reference with a coverageData >= 40X There is a 0.1% of reference with a coverageData >= 41X There is a 0.1% of reference with a coverageData >= 42X There is a 0.1% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.09% of reference with a coverageData >= 45X There is a 0.09% of reference with a coverageData >= 46X There is a 0.09% of reference with a coverageData >= 47X There is a 0.09% of reference with a coverageData >= 48X There is a 0.09% of reference with a coverageData >= 49X There is a 0.09% of reference with a coverageData >= 50X There is a 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 147013776 0.5898231082040113 32.257977624878194 chr2 243199373 127401141 0.5238547263853349 39.79133057745167 chr3 198022430 140094971 0.7074702143590501 43.99079217667636 chr4 191154276 54831688 0.28684520768973015 29.409562009313742 chr5 180915260 90157034 0.49833847072933485 34.531718496171294 chr6 171115067 68560547 0.4006692584236314 21.763002905262706 chr7 159138663 40120358 0.2521094323885328 13.845448135935824 chr8 146364022 57911227 0.3956657258298081 20.32429274027656 chr9 141213431 160114106 1.1338447403066072 72.12675546560091 chr10 135534747 57163339 0.42176150592585676 41.19208426274555 chr11 135006516 58587534 0.43396078749265704 27.030716045784974 chr12 133851895 113318746 0.8465979954934519 51.32442950111839 chr13 115169878 42199605 0.36641182341097905 49.75835396452492 chr14 107349540 31685434 0.2951613393033636 17.049541971834742 chr15 102531392 109155552 1.0646061647149 108.33794815179571 chr16 90354753 82615220 0.9143428237803937 50.23102012449343 chr17 81195210 70275044 0.8655072632979212 35.064853724874766 chr18 78077248 29567526 0.3786958013684089 37.31608206890656 chr19 59128983 62672436 1.0599275147350327 44.68600511347319 chr20 63025520 37357471 0.592735625188019 31.738746052179664 chr21 48129895 8284369 0.17212522487323106 13.988999370141295 chr22 51304566 32244967 0.6285009213409972 38.49773805241569 chrMT 16571 20188 1.218272886367751 1.379968682089548 chrX 155270560 151356150 0.9747897476508103 56.61507111575758 chrY 59373566 4215587 0.0710010747880631 4.327107629122503