BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708529.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,975,903 number of mapped reads = 2,682,121 (67.46%) number of supplementary alignments = 1,549 (0.04%) number of secondary alignments = 0 number of mapped bases = 126,498,623 bp number of sequenced bases = 126,467,466 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 111,838 duplication rate = 2.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.7719 >>>>>>> ACTG content number of A's = 35,723,485 bp (28.25%) number of C's = 23,205,254 bp (18.35%) number of T's = 40,549,084 bp (32.06%) number of G's = 26,987,994 bp (21.34%) number of N's = 1,649 bp (0%) GC percentage = 39.69% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 687,163 number of insertions = 7,700 mapped reads with insertion percentage = 0.29% number of deletions = 20,694 mapped reads with deletion percentage = 0.77% homopolymer indels = 47.04% >>>>>>> Coverage mean coverageData = 0.0409X std coverageData = 0.4337X There is a 3.66% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 10371798 0.04161192440920739 0.6706388785085319 chr2 243199373 11007250 0.04526019069958704 0.6535791788944812 chr3 198022430 8851868 0.04470134014616425 0.24690862281172762 chr4 191154276 8387291 0.0438770775915052 0.26347558068375887 chr5 180915260 7990427 0.044166683341139934 0.24184917811813872 chr6 171115067 7675334 0.04485481106114402 0.34655764540858813 chr7 159138663 7187598 0.04516563017750124 0.5393527339867273 chr8 146364022 6629675 0.045295796804490654 0.9267690483811906 chr9 141213431 5303462 0.03755635680291629 0.305442487705483 chr10 135534747 5903399 0.04355635090387559 0.3021665966623202 chr11 135006516 5903723 0.043729170820169895 0.3707252110387099 chr12 133851895 5859566 0.0437764889320394 0.24407090068587914 chr13 115169878 4052023 0.03518301026593082 0.2678494090667559 chr14 107349540 3989686 0.03716537583672925 0.23643432033556872 chr15 102531392 3671620 0.035809715721015475 0.22932908892706716 chr16 90354753 3361262 0.03720072147173044 0.2341134892918919 chr17 81195210 3309042 0.040754152861973016 0.3005945197772036 chr18 78077248 3364018 0.043085765522883186 0.490726463557274 chr19 59128983 2418215 0.040897287206850826 0.46983974371734394 chr20 63025520 2520414 0.039990372154009995 0.2291535593098903 chr21 48129895 1655668 0.03439999193848231 0.24050497538183496 chr22 51304566 1347310 0.026261015442563145 0.19212012097574888 chrMT 16571 173859 10.491762718001327 6.794905648577488 chrX 155270560 4574996 0.029464671216488172 0.24518314723470058 chrY 59373566 989119 0.01665924866294876 0.18235493763400049