BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082935.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 891,213 number of mapped reads = 806,941 (90.54%) number of supplementary alignments = 9,134 (1.02%) number of secondary alignments = 0 number of mapped bases = 55,171,254 bp number of sequenced bases = 55,150,803 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,569 duplication rate = 3.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9511 >>>>>>> ACTG content number of A's = 15,672,110 bp (28.42%) number of C's = 9,967,406 bp (18.07%) number of T's = 17,893,364 bp (32.44%) number of G's = 11,615,359 bp (21.06%) number of N's = 2,564 bp (0%) GC percentage = 39.13% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 404,719 number of insertions = 4,623 mapped reads with insertion percentage = 0.57% number of deletions = 12,600 mapped reads with deletion percentage = 1.55% homopolymer indels = 49.08% >>>>>>> Coverage mean coverageData = 0.0178X std coverageData = 0.1636X There is a 1.55% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.03% 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 5112967 0.02051335711616943 0.1975464906675191 chr2 243199373 5764534 0.023702914727498085 0.19874758272738477 chr3 198022430 3883880 0.01961333370164178 0.15737233728588257 chr4 191154276 2970412 0.015539343728831888 0.14139151123082305 chr5 180915260 3423259 0.01892189193990601 0.15478477674889576 chr6 171115067 4273823 0.02497631023923802 0.1854952201078027 chr7 159138663 2818484 0.0177108689168766 0.15548347301173632 chr8 146364022 5319293 0.03634289989653332 0.2652270929840761 chr9 141213431 1570040 0.011118205887937105 0.13168155500241693 chr10 135534747 1964338 0.014493242828719045 0.14166115973981175 chr11 135006516 1658749 0.01228643660428953 0.1291959847356772 chr12 133851895 1543605 0.011532186376591829 0.119740683597486 chr13 115169878 1269214 0.011020364196270139 0.11845618848719652 chr14 107349540 1275688 0.011883497591140121 0.12438820626179126 chr15 102531392 1172881 0.011439238043310677 0.12153508411923485 chr16 90354753 1877635 0.020780699826604583 0.16470215375710862 chr17 81195210 1388209 0.01709717851582624 0.15086885332625796 chr18 78077248 2236929 0.028650202937480582 0.23656021734886326 chr19 59128983 718112 0.01214483935906694 0.14126445415058728 chr20 63025520 770684 0.012228126003561731 0.1258834535547599 chr21 48129895 1018544 0.02116239813114074 0.1647434957329694 chr22 51304566 748144 0.014582405784311673 0.13560165017903836 chrMT 16571 8137 0.49103856134210366 0.7892129797302959 chrX 155270560 2294251 0.01477582743309485 0.13750787512819915 chrY 59373566 89442 0.0015064279615612105 0.043900806264831845