BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506018.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 1,445,379 number of mapped reads = 1,049,401 (72.6%) number of supplementary alignments = 70 (0%) number of secondary alignments = 0 number of mapped bases = 48,775,369 bp number of sequenced bases = 48,765,617 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,087 duplication rate = 2.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2398 >>>>>>> ACTG content number of A's = 14,315,872 bp (29.36%) number of C's = 10,068,161 bp (20.65%) number of T's = 14,066,845 bp (28.85%) number of G's = 10,154,313 bp (20.82%) number of N's = 160,426 bp (0.33%) GC percentage = 41.47% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 390,787 number of insertions = 2,080 mapped reads with insertion percentage = 0.2% number of deletions = 7,016 mapped reads with deletion percentage = 0.67% homopolymer indels = 45.94% >>>>>>> Coverage mean coverageData = 0.0158X std coverageData = 0.1846X There is a 1.41% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.02% 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 4737263 0.01900602285761206 0.31815006930542583 chr2 243199373 2932051 0.012056161838871189 0.14397421516077055 chr3 198022430 2912199 0.014706409773882686 0.13232645985758326 chr4 191154276 2097283 0.010971677138940905 0.1167828327644552 chr5 180915260 3570004 0.019733017546446883 0.1535250320630131 chr6 171115067 3375355 0.019725644615503087 0.17073337509666647 chr7 159138663 3154210 0.019820513384607233 0.31751273845115824 chr8 146364022 2762251 0.018872472635385766 0.2075772835719058 chr9 141213431 2309868 0.01635728261570247 0.15414807843095873 chr10 135534747 1592428 0.011749223245312879 0.1687265303617513 chr11 135006516 2525700 0.01870798591676864 0.17613063338846457 chr12 133851895 1433834 0.010712093392476812 0.11673749047006042 chr13 115169878 1541123 0.013381302704861769 0.12529706094208648 chr14 107349540 1710093 0.015930138126348747 0.15266862599262754 chr15 102531392 1616798 0.015768809614912865 0.13639881272653984 chr16 90354753 1457670 0.016132742900641872 0.14348122729395815 chr17 81195210 814986 0.010037365504689255 0.11706809755316133 chr18 78077248 1519369 0.01945981753865095 0.21471063446387287 chr19 59128983 1201486 0.020319747424033998 0.26358953873196417 chr20 63025520 1132535 0.01796946697147441 0.14762539246828488 chr21 48129895 688804 0.0143113547203874 0.13809436359559848 chr22 51304566 381851 0.0074428268236398296 0.09316166184197944 chrMT 16571 17098 1.0318025466175849 1.1335136865494573 chrX 155270560 3131273 0.0201665595847661 0.16649833287764731 chrY 59373566 159837 0.0026920565963647865 0.06941692210441418