BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094145.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 590,468 number of mapped reads = 552,487 (93.57%) number of supplementary alignments = 38,089 (6.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 277,679 number of mapped paired reads (second in pair) = 274,808 number of mapped paired reads (both in pair) = 547,358 number of mapped paired reads (singletons) = 5,129 number of mapped bases = 70,446,470 bp number of sequenced bases = 68,863,300 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 522,875 duplication rate = 50.55% >>>>>>> Insert size mean insert size = 1,546,765.162 std insert size = 11,133,359.8199 median insert size = 156 >>>>>>> Mapping quality mean mapping quality = 46.2774 >>>>>>> ACTG content number of A's = 19,042,940 bp (27.65%) number of C's = 15,435,239 bp (22.41%) number of T's = 18,038,845 bp (26.2%) number of G's = 16,345,378 bp (23.74%) number of N's = 898 bp (0%) GC percentage = 46.15% >>>>>>> Mismatches and indels general error rate = 0.0394 number of mismatches = 2,623,860 number of insertions = 43,738 mapped reads with insertion percentage = 7.77% number of deletions = 206,782 mapped reads with deletion percentage = 36.24% homopolymer indels = 29.22% >>>>>>> Coverage mean coverageData = 0.0228X std coverageData = 4.0548X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1161023 0.004658054593171907 1.328626812773683 chr2 243199373 3169854 0.013033972747947833 3.553095541119556 chr3 198022430 1059295 0.005349368755852557 1.36699469911845 chr4 191154276 1271739 0.006652945602953711 1.5849996028147115 chr5 180915260 1515703 0.008377972095886218 2.5613828338373494 chr6 171115067 936128 0.0054707514446989056 1.6617006092117053 chr7 159138663 1626267 0.01021918224862804 2.5305536158026105 chr8 146364022 1361720 0.009303652505531721 2.530419521899328 chr9 141213431 1054261 0.00746572753408987 2.4774644745778103 chr10 135534747 978981 0.0072230997708654 1.5734225258554624 chr11 135006516 1340682 0.0099304984657185 2.334557100373333 chr12 133851895 1570873 0.01173590407517204 2.5817645654206203 chr13 115169878 1325626 0.011510179771137727 2.328985756286114 chr14 107349540 282951 0.002635791452855783 0.7688444345161928 chr15 102531392 772781 0.007537018516241348 1.674531073433702 chr16 90354753 347690 0.0038480543464049976 1.0831141326521063 chr17 81195210 953219 0.011739842781366043 2.276773102606948 chr18 78077248 312093 0.003997233611512537 0.884473050591218 chr19 59128983 218829 0.0037008754234788715 0.8590850373556086 chr20 63025520 456462 0.007242494786238971 2.3443234051356563 chr21 48129895 396407 0.00823619083316097 2.5430098613428673 chr22 51304566 244094 0.004757744174270961 1.127966734682112 chrMT 16571 4071264 245.68607808822642 973.0332938612205 chrX 155270560 44008487 0.28343098009049494 11.647213650286057 chrY 59373566 10041 1.6911566335766324E-4 0.06766118346900564