BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549010.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 9,128,073 number of mapped reads = 7,912,765 (86.69%) number of secondary alignments = 0 number of mapped bases = 313,998,417 bp number of sequenced bases = 313,963,039 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 613,802 duplication rate = 6.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6277 >>>>>>> ACTG content number of A's = 93,695,044 bp (29.84%) number of C's = 62,840,554 bp (20.02%) number of T's = 93,627,088 bp (29.82%) number of G's = 63,797,327 bp (20.32%) number of N's = 3,026 bp (0%) GC percentage = 40.34% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 954,756 number of insertions = 9,872 mapped reads with insertion percentage = 0.12% number of deletions = 27,344 mapped reads with deletion percentage = 0.35% homopolymer indels = 42.13% >>>>>>> Coverage mean coverageData = 0.1014X std coverageData = 0.7811X There is a 7.87% of reference with a coverageData >= 1X There is a 1.63% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 25273238 0.10139689080253084 1.1567352774140174 chr2 243199373 27400938 0.11266862106589395 0.5808302907414541 chr3 198022430 22093298 0.11156967420306882 0.40663926505866643 chr4 191154276 21755783 0.11381269336606417 0.4601532822073224 chr5 180915260 20205843 0.11168678087188444 0.4139824827122945 chr6 171115067 19175240 0.11206050020130606 0.4860761667369774 chr7 159138663 17640151 0.11084767628090479 0.8577129027208121 chr8 146364022 16507293 0.11278245004773099 2.2715956939367246 chr9 141213431 13434806 0.09513830168179965 0.5421456009654522 chr10 135534747 14947091 0.11028235438400162 0.6310510479751495 chr11 135006516 14614078 0.10824720489787322 0.5353853224013742 chr12 133851895 14534055 0.1085831097124176 0.419704692435302 chr13 115169878 10628788 0.09228791576908678 0.36670535552307765 chr14 107349540 9916114 0.09237220764988839 0.4692249845908856 chr15 102531392 8899039 0.08679331106711201 0.35674833470921696 chr16 90354753 8350583 0.09241996378430695 0.4243992808039764 chr17 81195210 7645321 0.09415975400519316 0.4175490211840379 chr18 78077248 8702710 0.11146281692715398 1.1199608439794864 chr19 59128983 5259356 0.08894717502582447 0.9223755587226575 chr20 63025520 6300550 0.09996823508953198 0.41410639728170456 chr21 48129895 4102509 0.08523827030996016 0.4421406622153488 chr22 51304566 3185638 0.062092680016043796 0.3327049774412586 chrMT 16571 13633 0.8227023112666707 1.3686115385049171 chrX 155270560 10643157 0.06854587888393009 0.42069123755781473 chrY 59373566 2769205 0.046640368543806175 0.47259680120298125