BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472411.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 20,193,570 number of mapped reads = 19,961,104 (98.85%) number of supplementary alignments = 74,007 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,030,488 number of mapped paired reads (second in pair) = 9,930,616 number of mapped paired reads (both in pair) = 19,806,864 number of mapped paired reads (singletons) = 154,240 number of mapped bases = 1,955,547,086 bp number of sequenced bases = 1,955,311,460 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,870,612 duplication rate = 48.8% >>>>>>> Insert size mean insert size = 19,166.0375 std insert size = 1,380,855.3094 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 55.263 >>>>>>> ACTG content number of A's = 524,073,510 bp (26.8%) number of C's = 454,897,609 bp (23.26%) number of T's = 524,853,304 bp (26.84%) number of G's = 451,239,776 bp (23.08%) number of N's = 247,261 bp (0.01%) GC percentage = 46.34% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 10,792,879 number of insertions = 108,243 mapped reads with insertion percentage = 0.53% number of deletions = 93,201 mapped reads with deletion percentage = 0.46% homopolymer indels = 44.76% >>>>>>> Coverage mean coverageData = 0.6317X std coverageData = 19.0633X There is a 5.26% of reference with a coverageData >= 1X There is a 2.34% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.72% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.48% of reference with a coverageData >= 6X There is a 0.44% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.4% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.36% of reference with a coverageData >= 12X There is a 0.35% of reference with a coverageData >= 13X There is a 0.34% of reference with a coverageData >= 14X There is a 0.33% of reference with a coverageData >= 15X There is a 0.32% of reference with a coverageData >= 16X There is a 0.32% of reference with a coverageData >= 17X There is a 0.31% of reference with a coverageData >= 18X There is a 0.3% of reference with a coverageData >= 19X There is a 0.3% of reference with a coverageData >= 20X There is a 0.29% of reference with a coverageData >= 21X There is a 0.29% of reference with a coverageData >= 22X There is a 0.28% of reference with a coverageData >= 23X There is a 0.28% of reference with a coverageData >= 24X There is a 0.27% of reference with a coverageData >= 25X There is a 0.27% of reference with a coverageData >= 26X There is a 0.26% of reference with a coverageData >= 27X There is a 0.26% of reference with a coverageData >= 28X There is a 0.25% of reference with a coverageData >= 29X There is a 0.25% of reference with a coverageData >= 30X There is a 0.25% of reference with a coverageData >= 31X There is a 0.24% of reference with a coverageData >= 32X There is a 0.24% of reference with a coverageData >= 33X There is a 0.24% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.23% of reference with a coverageData >= 36X There is a 0.23% of reference with a coverageData >= 37X There is a 0.22% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.22% of reference with a coverageData >= 40X There is a 0.22% of reference with a coverageData >= 41X There is a 0.21% of reference with a coverageData >= 42X There is a 0.21% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.21% of reference with a coverageData >= 45X There is a 0.2% of reference with a coverageData >= 46X There is a 0.2% of reference with a coverageData >= 47X There is a 0.2% of reference with a coverageData >= 48X There is a 0.2% of reference with a coverageData >= 49X There is a 0.2% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 214441263 0.8603439467458739 23.889462800479485 chr2 243199373 141143104 0.5803596541344701 17.138494072785083 chr3 198022430 161472594 0.8154257777767903 19.440719701792563 chr4 191154276 70224716 0.3673719336521669 14.703487450947438 chr5 180915260 98512367 0.5445221536314847 16.80292122079204 chr6 171115067 128638766 0.751767616115301 19.500356752957416 chr7 159138663 105091328 0.6603758383969834 18.36207684514207 chr8 146364022 119507798 0.8165107542617269 23.397813566485436 chr9 141213431 101895807 0.7215730563192675 21.277834914978335 chr10 135534747 50336433 0.3713913525068225 12.06692665208183 chr11 135006516 69167120 0.5123243088503965 15.682829405113123 chr12 133851895 102343115 0.7645996718985563 21.941001185019747 chr13 115169878 42721899 0.3709468112834156 12.31235341857451 chr14 107349540 50582953 0.4711986003852462 16.389925604482933 chr15 102531392 51459717 0.5018923082600888 17.23426418496301 chr16 90354753 103934460 1.150293222538055 30.651312830001597 chr17 81195210 97263707 1.197899568213445 28.109532203696524 chr18 78077248 41155337 0.5271104970298134 18.81417022404041 chr19 59128983 43760291 0.7400819154965003 22.359562760971528 chr20 63025520 36479700 0.5788083938061915 15.34269915313644 chr21 48129895 18425231 0.38282300428870664 23.119748627218655 chr22 51304566 23095532 0.45016523480580656 13.093282059755179 chrMT 16571 7867 0.4747450365095649 0.9047371557359175 chrX 155270560 81696456 0.5261554798282431 14.183209750916166 chrY 59373566 2189525 0.03687710116653596 1.731609444065701