BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3212175.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 = 6,714,736 number of mapped reads = 5,526,743 (82.31%) number of supplementary alignments = 42,412 (0.63%) number of secondary alignments = 0 number of mapped bases = 356,408,551 bp number of sequenced bases = 356,282,768 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 349,823 duplication rate = 4.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8893 >>>>>>> ACTG content number of A's = 100,397,228 bp (28.18%) number of C's = 69,406,786 bp (19.48%) number of T's = 109,300,055 bp (30.68%) number of G's = 77,092,155 bp (21.64%) number of N's = 86,544 bp (0.02%) GC percentage = 41.12% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 3,932,851 number of insertions = 26,651 mapped reads with insertion percentage = 0.48% number of deletions = 79,695 mapped reads with deletion percentage = 1.43% homopolymer indels = 45.91% >>>>>>> Coverage mean coverageData = 0.1151X std coverageData = 1.1017X There is a 8.53% of reference with a coverageData >= 1X There is a 1.98% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% 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% 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 38651322 0.15507011314527477 2.4158929295302425 chr2 243199373 23631371 0.09716871679599273 0.7340147167192549 chr3 198022430 24260094 0.12251184878399886 0.4707320166802549 chr4 191154276 15858664 0.08296264322122723 0.38246010739353514 chr5 180915260 20876607 0.11539439514389223 0.43301007118921353 chr6 171115067 26118276 0.15263574656462017 0.7078833697834209 chr7 159138663 24721284 0.15534429870131558 2.08421628209672 chr8 146364022 22872236 0.1562695236675035 1.5772779422685375 chr9 141213431 10068133 0.07129727624846109 0.632628889216565 chr10 135534747 12125705 0.08946565562261315 1.2710049994713901 chr11 135006516 15314913 0.113438324710194 0.8390635990931948 chr12 133851895 10690192 0.07986582483572609 0.38558518989657786 chr13 115169878 10573502 0.09180787705618651 0.3795627391926874 chr14 107349540 14158738 0.1318937929310177 0.741777143123649 chr15 102531392 6498959 0.06338506552217686 0.3099148785494319 chr16 90354753 12454177 0.1378364345702987 0.5353386012281466 chr17 81195210 6104957 0.0751886348960733 0.46387055954713136 chr18 78077248 8740060 0.1119411893206072 1.2518188374349155 chr19 59128983 8913593 0.15074828870302065 1.75624716300363 chr20 63025520 9035218 0.14335808732716526 0.49800036927735264 chr21 48129895 5677257 0.11795697871354176 0.4718805908145834 chr22 51304566 2717515 0.052968287461977556 0.28454456609099693 chrMT 16571 299976 18.10246816728019 10.910570830460708 chrX 155270560 25076508 0.16150201300233605 0.5999973724619081 chrY 59373566 969294 0.016325345861826792 0.23388067988600694