BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081208.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 = 6,020,345 number of mapped reads = 4,857,421 (80.68%) number of supplementary alignments = 54,683 (0.91%) number of secondary alignments = 0 number of mapped bases = 327,013,764 bp number of sequenced bases = 326,898,051 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 596,848 duplication rate = 8.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3537 >>>>>>> ACTG content number of A's = 89,029,544 bp (27.23%) number of C's = 64,799,459 bp (19.82%) number of T's = 99,395,099 bp (30.41%) number of G's = 73,498,076 bp (22.48%) number of N's = 175,873 bp (0.05%) GC percentage = 42.31% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 3,272,371 number of insertions = 23,234 mapped reads with insertion percentage = 0.47% number of deletions = 71,637 mapped reads with deletion percentage = 1.46% homopolymer indels = 46.35% >>>>>>> Coverage mean coverageData = 0.1056X std coverageData = 0.9485X There is a 6.2% of reference with a coverageData >= 1X There is a 2.38% of reference with a coverageData >= 2X There is a 1% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.19% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% 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% 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 32603849 0.13080749355485055 1.7699511343644898 chr2 243199373 19934972 0.08196966856489388 0.787030573487944 chr3 198022430 20812672 0.10510259873086095 0.4986510321298633 chr4 191154276 12987951 0.06794486250467136 0.42231817449456815 chr5 180915260 22482707 0.124272032110503 0.5451874716387302 chr6 171115067 20526542 0.11995753711156248 0.6636737614099115 chr7 159138663 19786897 0.12433745908748775 1.1910359968228548 chr8 146364022 20255269 0.13838967201926167 1.398536136982093 chr9 141213431 16513512 0.11694009474212123 0.7374727479089074 chr10 135534747 9843376 0.07262621739353672 0.8275841592742136 chr11 135006516 17534799 0.1298811310707403 0.7788009509859949 chr12 133851895 9414998 0.07033892198537794 0.42229674389455285 chr13 115169878 9086381 0.07889546431576493 0.426060911325618 chr14 107349540 12153165 0.11321115116096446 2.0000715641955207 chr15 102531392 11379724 0.11098770608712695 0.5102354975980061 chr16 90354753 11895219 0.1316501745071452 0.6013649856092574 chr17 81195210 5447330 0.06708930243545155 0.44237867881084547 chr18 78077248 9166886 0.11740790351627148 1.2216324182753198 chr19 59128983 8195575 0.13860503908886782 1.33050020296394 chr20 63025520 9023398 0.14317054424937709 0.6196676121468205 chr21 48129895 5062234 0.10517857975796539 0.5337855413411333 chr22 51304566 2965823 0.0578081685750933 0.36672131381309825 chrMT 16571 51087 3.082915937481142 2.715062955667719 chrX 155270560 19135702 0.12324101877393887 0.6009694924114795 chrY 59373566 753696 0.012694133951799358 0.24011424964645117