BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714147.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 756,984 number of mapped reads = 537,778 (71.04%) number of supplementary alignments = 17,399 (2.3%) number of secondary alignments = 0 number of mapped bases = 69,968,877 bp number of sequenced bases = 68,220,214 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 478,929 duplication rate = 43.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.2901 >>>>>>> ACTG content number of A's = 18,654,036 bp (27.34%) number of C's = 13,861,246 bp (20.32%) number of T's = 17,736,898 bp (26%) number of G's = 17,967,218 bp (26.34%) number of N's = 816 bp (0%) GC percentage = 46.66% >>>>>>> Mismatches and indels general error rate = 0.0476 number of mismatches = 3,065,446 number of insertions = 71,228 mapped reads with insertion percentage = 12.65% number of deletions = 270,821 mapped reads with deletion percentage = 46.53% homopolymer indels = 31.14% >>>>>>> Coverage mean coverageData = 0.0226X std coverageData = 6.238X There is a 0.06% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4099449 0.016447096434716604 3.0397883761832643 chr2 243199373 9469067 0.03893540876850863 16.618262728201195 chr3 198022430 3685213 0.01861007866634098 3.4401866151547744 chr4 191154276 2290286 0.011981348510351921 2.0553314937930676 chr5 180915260 3681098 0.020347084043656684 3.3306404588690586 chr6 171115067 2640147 0.015429073817327846 2.3926309395767484 chr7 159138663 3019237 0.018972366256464025 3.582381000826454 chr8 146364022 4852896 0.03315634493837563 10.310980786141707 chr9 141213431 2400968 0.01700240538734591 2.339011088736327 chr10 135534747 2959635 0.021836725013401913 3.1946796891071534 chr11 135006516 3836517 0.028417272837408827 6.211071508941912 chr12 133851895 3074327 0.02296812458277113 3.6533420318088625 chr13 115169878 2797856 0.02429329655103047 5.4448687600174 chr14 107349540 2452090 0.022842109989479227 5.447950711189239 chr15 102531392 1972860 0.019241521660019988 2.584931027484515 chr16 90354753 1850539 0.02048081521511104 2.5225627124984347 chr17 81195210 1711587 0.0210799011419516 3.932134113434184 chr18 78077248 1502012 0.01923751205985129 3.0049691063704898 chr19 59128983 1475799 0.02495897823914881 4.230930336595387 chr20 63025520 1549813 0.02459024534823354 5.386154752862854 chr21 48129895 588936 0.012236386553513154 1.8191679666615268 chr22 51304566 631195 0.012302901071222394 2.0440533979684368 chrMT 16571 560276 33.81063303361294 261.4039560843017 chrX 155270560 6661553 0.04290287225086327 4.975187550839557 chrY 59373566 205521 0.003461489916236461 0.6773310573360528