BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505921.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 = 6,446,188 number of mapped reads = 4,606,889 (71.47%) number of supplementary alignments = 237 (0%) number of secondary alignments = 0 number of mapped bases = 212,654,793 bp number of sequenced bases = 212,612,450 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 219,411 duplication rate = 3.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5082 >>>>>>> ACTG content number of A's = 62,472,418 bp (29.38%) number of C's = 43,979,095 bp (20.69%) number of T's = 61,830,646 bp (29.08%) number of G's = 44,329,621 bp (20.85%) number of N's = 670 bp (0%) GC percentage = 41.54% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,063,032 number of insertions = 9,286 mapped reads with insertion percentage = 0.2% number of deletions = 30,567 mapped reads with deletion percentage = 0.66% homopolymer indels = 45.87% >>>>>>> Coverage mean coverageData = 0.0687X std coverageData = 0.5957X There is a 5.56% of reference with a coverageData >= 1X There is a 0.93% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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% 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 22581621 0.0905980531137774 1.291779611144595 chr2 243199373 13801183 0.05674843166639249 0.44035858750648066 chr3 198022430 14161124 0.07151272711884205 0.32046466359222486 chr4 191154276 9717206 0.05083436375757558 0.2723130018667135 chr5 180915260 12194503 0.0674045019751236 0.31303883875137645 chr6 171115067 14979382 0.08753981903884595 0.4703536539156284 chr7 159138663 14541265 0.09137480940128295 0.8938897023528165 chr8 146364022 13260679 0.09060067370928082 0.8270580456456331 chr9 141213431 5999755 0.0424871413258134 0.36364516905884425 chr10 135534747 6923373 0.0510819044801847 0.6163512752152284 chr11 135006516 11804797 0.08743872036517111 0.498113427460668 chr12 133851895 6392203 0.047755790084256934 0.27817713647467074 chr13 115169878 6072120 0.05272316082509005 0.26925602577840785 chr14 107349540 8133131 0.07576307266896533 0.5045648536079601 chr15 102531392 4048853 0.03948891086936575 0.23153160812268847 chr16 90354753 7250020 0.08023949774949858 0.4027532299214885 chr17 81195210 3647373 0.04492103659809489 0.2813323490006124 chr18 78077248 5560839 0.071222272075983 0.7065559992510195 chr19 59128983 5518427 0.09332863039433639 0.9847617622711323 chr20 63025520 5576453 0.0884792858511917 0.3611634097725189 chr21 48129895 3264632 0.06782960985059286 0.3279519233538895 chr22 51304566 1517170 0.029571831871650568 0.20197381046759277 chrMT 16571 8585 0.5180737432864643 0.8732823156504215 chrX 155270560 15064741 0.09702251991620305 0.42033145188559207 chrY 59373566 635358 0.010701024762433842 0.1540054577227545