BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472837.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 = 3,084,403 number of mapped reads = 2,469,050 (80.05%) number of supplementary alignments = 21,547 (0.7%) number of secondary alignments = 0 number of mapped bases = 160,012,317 bp number of sequenced bases = 159,946,544 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,606 duplication rate = 2.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.176 >>>>>>> ACTG content number of A's = 43,339,621 bp (27.1%) number of C's = 31,653,816 bp (19.79%) number of T's = 47,792,250 bp (29.88%) number of G's = 37,157,871 bp (23.23%) number of N's = 2,986 bp (0%) GC percentage = 43.02% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,379,268 number of insertions = 12,688 mapped reads with insertion percentage = 0.51% number of deletions = 36,997 mapped reads with deletion percentage = 1.48% homopolymer indels = 45.27% >>>>>>> Coverage mean coverageData = 0.0517X std coverageData = 0.3818X There is a 4.47% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 11670281 0.04682147211179867 0.5059102328762288 chr2 243199373 15306278 0.06293716061513037 0.5899181761184891 chr3 198022430 11854593 0.05986490015297762 0.27338193823537893 chr4 191154276 8834621 0.04621722927087438 0.27495634762688037 chr5 180915260 8089832 0.04471613947878139 0.2394296755547278 chr6 171115067 9757507 0.05702307325163833 0.2974433911898384 chr7 159138663 9837726 0.06181857893326652 0.4973965722283508 chr8 146364022 8994680 0.06145417348533918 0.3849804666783203 chr9 141213431 9182324 0.06502443807912295 0.44850045595001475 chr10 135534747 6555136 0.04836498495843284 0.3693902798981472 chr11 135006516 5229481 0.03873502668567493 0.3443751804551479 chr12 133851895 6676646 0.049880847783290626 0.2587062603340603 chr13 115169878 6501874 0.05645463998841781 0.2757593406272998 chr14 107349540 3252985 0.030302738139352997 0.2322547855500897 chr15 102531392 3097383 0.03020911878383549 0.21659912155379668 chr16 90354753 5277140 0.05840467518072901 0.30609838399905326 chr17 81195210 3506185 0.043182165548928314 0.2583844730085469 chr18 78077248 2763962 0.035400351200902985 0.7088284991243141 chr19 59128983 3711693 0.06277281988766828 0.40432573138137173 chr20 63025520 7115737 0.11290247188757824 0.40085192861844693 chr21 48129895 1956663 0.040653797395568805 0.2750441761515537 chr22 51304566 1845350 0.03596853348296524 0.22547175686779122 chrMT 16571 16810 1.0144227867962103 1.244493799915144 chrX 155270560 8131331 0.052368787747013985 0.2982033676938235 chrY 59373566 846099 0.0142504325915004 0.19320626427362822