BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082951.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 = 1,577,017 number of mapped reads = 1,455,292 (92.28%) number of supplementary alignments = 13,722 (0.87%) number of secondary alignments = 0 number of mapped bases = 97,825,470 bp number of sequenced bases = 97,787,016 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,924 duplication rate = 3.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.912 >>>>>>> ACTG content number of A's = 27,294,555 bp (27.91%) number of C's = 17,835,087 bp (18.24%) number of T's = 31,338,836 bp (32.05%) number of G's = 21,313,332 bp (21.8%) number of N's = 5,206 bp (0.01%) GC percentage = 40.03% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 693,591 number of insertions = 8,548 mapped reads with insertion percentage = 0.58% number of deletions = 23,481 mapped reads with deletion percentage = 1.6% homopolymer indels = 48.62% >>>>>>> Coverage mean coverageData = 0.0316X std coverageData = 0.3048X There is a 2.72% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 8936551 0.03585367596737101 0.5218521542279603 chr2 243199373 9591419 0.039438502170809464 0.3980225972804041 chr3 198022430 6766903 0.0341724066309054 0.20741065053966415 chr4 191154276 7124407 0.037270455828045404 0.2238165411072504 chr5 180915260 5460781 0.03018419231191443 0.19640347303284855 chr6 171115067 6349389 0.03710596098472147 0.26645564750159656 chr7 159138663 5635231 0.03541082282436921 0.38529216767321184 chr8 146364022 8118529 0.055468064412714756 0.39110062509773713 chr9 141213431 2790662 0.019762015413392228 0.2567388040347404 chr10 135534747 3738707 0.02758485984409592 0.21932011998446493 chr11 135006516 3525664 0.02611476915677166 0.240505660774722 chr12 133851895 2972988 0.02221102659771832 0.17125326716507192 chr13 115169878 2180148 0.01892984552783845 0.15568709789435128 chr14 107349540 1975251 0.018400181314237582 0.17557592146591308 chr15 102531392 1897505 0.0185065760152754 0.15882221660615026 chr16 90354753 3867177 0.04279992885377042 0.24727528784745717 chr17 81195210 2257024 0.027797501847707518 0.20583993880305682 chr18 78077248 3341765 0.04280075291588146 0.6304334797008004 chr19 59128983 1433693 0.024246873990712813 0.34671088946930284 chr20 63025520 1659856 0.026336252362535048 0.19434583004919712 chr21 48129895 2703747 0.056176041938175846 0.27252343350108266 chr22 51304566 1281337 0.02497510650416573 0.17648643439251083 chrMT 16571 26499 1.5991189427312775 1.6055941502362343 chrX 155270560 4011176 0.025833461282035692 0.20232484421365524 chrY 59373566 179061 0.003015837047752867 0.06956035634915873