BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717050.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 990,841 number of mapped reads = 803,346 (81.08%) number of supplementary alignments = 2,772 (0.28%) number of secondary alignments = 0 number of mapped bases = 45,045,331 bp number of sequenced bases = 45,032,085 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,804 duplication rate = 1.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.3151 >>>>>>> ACTG content number of A's = 10,999,564 bp (24.43%) number of C's = 8,646,527 bp (19.2%) number of T's = 13,493,305 bp (29.96%) number of G's = 11,891,452 bp (26.41%) number of N's = 1,237 bp (0%) GC percentage = 45.61% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 235,824 number of insertions = 3,546 mapped reads with insertion percentage = 0.44% number of deletions = 7,713 mapped reads with deletion percentage = 0.95% homopolymer indels = 34.73% >>>>>>> Coverage mean coverageData = 0.0146X std coverageData = 0.1491X There is a 1.34% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4357693 0.017483178106103895 0.18413641431971006 chr2 243199373 3892409 0.016005012480028065 0.17905631505848524 chr3 198022430 3064083 0.015473413794588825 0.13524904013588554 chr4 191154276 2961059 0.015490414663807992 0.15151054186320093 chr5 180915260 2769968 0.015310858796543751 0.132414345516369 chr6 171115067 1916960 0.01120275399243481 0.11428616829898368 chr7 159138663 2629171 0.016521258570583817 0.16842544507784407 chr8 146364022 2754633 0.01882042432531678 0.151832112214966 chr9 141213431 2012193 0.014249303240851077 0.13793083414974788 chr10 135534747 2394678 0.01766836957315455 0.2205292237956667 chr11 135006516 1853214 0.013726848561887191 0.14559219963020748 chr12 133851895 2184516 0.016320396509888785 0.1372935443466326 chr13 115169878 790431 0.006863174761720247 0.09048776409282971 chr14 107349540 1425612 0.013280094167147805 0.12576344471268394 chr15 102531392 881387 0.00859626483955275 0.100421816170568 chr16 90354753 1188662 0.013155500519159187 0.13078174140103818 chr17 81195210 1742306 0.021458236267878364 0.16197526560040418 chr18 78077248 1195961 0.015317663347970462 0.1628456276902683 chr19 59128983 1172393 0.01982772137312086 0.17356273095678285 chr20 63025520 1127439 0.017888610835737652 0.14926808325985924 chr21 48129895 607629 0.012624773023086795 0.13251846635683043 chr22 51304566 485214 0.009457520798441215 0.1061606326088332 chrMT 16571 35459 2.13982258161849 2.1244280917977463 chrX 155270560 1451397 0.009347535038193976 0.10942628808767531 chrY 59373566 150864 0.0025409287358620163 0.09096877989822506