BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548980.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 = 6,819,273 number of mapped reads = 3,016,940 (44.24%) number of secondary alignments = 0 number of mapped bases = 119,504,988 bp number of sequenced bases = 119,490,834 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,957 duplication rate = 1.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1734 >>>>>>> ACTG content number of A's = 35,074,804 bp (29.35%) number of C's = 24,324,746 bp (20.36%) number of T's = 35,433,984 bp (29.65%) number of G's = 24,650,794 bp (20.63%) number of N's = 6,506 bp (0.01%) GC percentage = 40.99% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 333,320 number of insertions = 3,792 mapped reads with insertion percentage = 0.13% number of deletions = 11,213 mapped reads with deletion percentage = 0.37% homopolymer indels = 45.74% >>>>>>> Coverage mean coverageData = 0.0386X std coverageData = 0.2963X There is a 3.44% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 9530463 0.038236466419877047 0.4891569449638606 chr2 243199373 10580713 0.043506333381871015 0.28915210557946436 chr3 198022430 8299538 0.04191211066342333 0.2236449851070223 chr4 191154276 8073430 0.04223515251105343 0.228530179249681 chr5 180915260 7560679 0.041791272886543676 0.2265306826803301 chr6 171115067 7409964 0.04330398327810607 0.25775263115678554 chr7 159138663 6891041 0.04330211697203966 0.4451737092259021 chr8 146364022 6131644 0.04189310949654007 0.38701420553355187 chr9 141213431 5146193 0.036442659622086516 0.26314302369631726 chr10 135534747 5344289 0.039431135692458257 0.2525428083513866 chr11 135006516 5480082 0.04059124079611091 0.27054497209569334 chr12 133851895 5622241 0.04200344716823023 0.22939691241200505 chr13 115169878 4054894 0.035207938659099734 0.20427255617235246 chr14 107349540 3517622 0.032767928022793574 0.21640485603099616 chr15 102531392 3502193 0.0341572754615484 0.2015700525606433 chr16 90354753 3402106 0.037652761886250746 0.22226371672387332 chr17 81195210 3143475 0.03871503011076639 0.22785413442519725 chr18 78077248 3172463 0.04063236193980607 0.4221925721186642 chr19 59128983 2269382 0.03838019673025663 0.42509233965601545 chr20 63025520 2456103 0.038969975971638156 0.22077822767173289 chr21 48129895 1558804 0.032387438202389596 0.21342563533620418 chr22 51304566 1384375 0.026983465760143065 0.18910077781272536 chrMT 16571 2334 0.1408484702190574 0.45211601082388103 chrX 155270560 4038521 0.02600957322495649 0.2025332651511362 chrY 59373566 932439 0.015704615080724644 0.16829079041736905