BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006384.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 = 4,988,012 number of mapped reads = 875,167 (17.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 444,423 number of mapped paired reads (second in pair) = 430,744 number of mapped paired reads (both in pair) = 770,806 number of mapped paired reads (singletons) = 104,361 number of mapped bases = 33,852,108 bp number of sequenced bases = 33,847,628 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,553 duplication rate = 2.41% >>>>>>> Insert size mean insert size = 74,491.8452 std insert size = 2,590,690.215 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 47.7348 >>>>>>> ACTG content number of A's = 9,426,344 bp (27.85%) number of C's = 7,311,678 bp (21.6%) number of T's = 9,563,494 bp (28.25%) number of G's = 7,544,733 bp (22.29%) number of N's = 1,379 bp (0%) GC percentage = 43.89% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 127,904 number of insertions = 1,105 mapped reads with insertion percentage = 0.13% number of deletions = 3,345 mapped reads with deletion percentage = 0.38% homopolymer indels = 40.67% >>>>>>> Coverage mean coverageData = 0.0109X std coverageData = 0.1622X There is a 1.02% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0% 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 2742215 0.011001838185991921 0.16971674678627247 chr2 243199373 2856888 0.011747102653920082 0.26192990782046677 chr3 198022430 2258893 0.011407258258572021 0.11236318716785847 chr4 191154276 2086993 0.010917846274074454 0.11334408320168327 chr5 180915260 2066788 0.011424066714991316 0.3248418972652441 chr6 171115067 1933167 0.01129746803652305 0.17500133594182726 chr7 159138663 1803894 0.011335359779917216 0.12242609848684957 chr8 146364022 1752046 0.011970469081534258 0.1831371174345699 chr9 141213431 1417049 0.01003480327590086 0.10746347542064501 chr10 135534747 1571397 0.011594052704433056 0.1250635922077127 chr11 135006516 1574556 0.011662814852580894 0.14484747659626418 chr12 133851895 1544049 0.011535503475688559 0.11346110428728376 chr13 115169878 1046757 0.009088808794257818 0.10022903731944828 chr14 107349540 1048051 0.009762976161798179 0.10891734480520364 chr15 102531392 1000473 0.009757723761323752 0.10381923278827408 chr16 90354753 993443 0.010994916891643763 0.11464234838030325 chr17 81195210 958273 0.011802087832521155 0.11993678654147896 chr18 78077248 879093 0.011259272355501055 0.12587648190656614 chr19 59128983 710324 0.012013127301715979 0.12286020161461572 chr20 63025520 766856 0.012167388702227288 0.11712976436562833 chr21 48129895 469624 0.009757428309369884 0.14657218614420722 chr22 51304566 444193 0.008657962334190684 0.09915858215356095 chrMT 16571 466 0.028121416933196548 0.1783149897645929 chrX 155270560 1842730 0.011867864713053138 0.1168098655224456 chrY 59373566 83890 0.0014129183347350233 0.04950449571308694