BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708632.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 = 2,695,197 number of mapped reads = 1,916,021 (71.09%) number of supplementary alignments = 570 (0.02%) number of secondary alignments = 0 number of mapped bases = 93,179,643 bp number of sequenced bases = 93,161,901 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,883 duplication rate = 2.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3006 >>>>>>> ACTG content number of A's = 27,464,889 bp (29.48%) number of C's = 17,445,218 bp (18.73%) number of T's = 29,463,699 bp (31.63%) number of G's = 18,779,832 bp (20.16%) number of N's = 8,263 bp (0.01%) GC percentage = 38.88% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 595,975 number of insertions = 4,252 mapped reads with insertion percentage = 0.22% number of deletions = 11,713 mapped reads with deletion percentage = 0.61% homopolymer indels = 48.01% >>>>>>> Coverage mean coverageData = 0.0301X std coverageData = 0.3059X There is a 2.67% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.03% 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 7361188 0.02953327847476055 0.5456556484424404 chr2 243199373 8076942 0.03321119581998264 0.3221432960975361 chr3 198022430 6558284 0.033118894662589486 0.20177482021349566 chr4 191154276 6348455 0.03321115871873041 0.20484042298688374 chr5 180915260 5890524 0.03255957512926218 0.20260746920461903 chr6 171115067 5527803 0.03230459536330603 0.24470342728304367 chr7 159138663 5276654 0.03315758660106375 0.433566626183384 chr8 146364022 4916548 0.03359123323353331 0.4838912586526034 chr9 141213431 3922465 0.027776855021672833 0.2541194515609405 chr10 135534747 4246827 0.03133386156687923 0.2509338860537918 chr11 135006516 4107694 0.03042589440645961 0.25634588231890576 chr12 133851895 4243298 0.03170144135800244 0.20254122271281616 chr13 115169878 3078849 0.02673310985012939 0.18191595776027253 chr14 107349540 2903591 0.027048005981208677 0.19321541901041314 chr15 102531392 2494848 0.024332528324593507 0.17135947061478654 chr16 90354753 2386800 0.026415876539444473 0.18840264836883153 chr17 81195210 2187846 0.026945505775525427 0.20766592290903407 chr18 78077248 2615370 0.03349721035249603 0.5124963701551185 chr19 59128983 1500781 0.025381478318340093 0.3803776838098867 chr20 63025520 1822410 0.02891542981319313 0.19250831057136492 chr21 48129895 1214141 0.025226338017151295 0.1864028464577618 chr22 51304566 893292 0.017411549685460746 0.14315635519426767 chrMT 16571 6275 0.3786735863858548 0.6819669697914956 chrX 155270560 5372589 0.034601465982991235 0.22959887081281993 chrY 59373566 226169 0.0038092541047643996 0.0801256143408635