BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717003.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 = 2,088,062 number of mapped reads = 1,884,421 (90.25%) number of supplementary alignments = 9,650 (0.46%) number of secondary alignments = 0 number of mapped bases = 108,249,656 bp number of sequenced bases = 108,218,459 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,073 duplication rate = 2.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4571 >>>>>>> ACTG content number of A's = 28,070,371 bp (25.94%) number of C's = 20,862,210 bp (19.28%) number of T's = 33,925,281 bp (31.35%) number of G's = 25,358,825 bp (23.43%) number of N's = 1,772 bp (0%) GC percentage = 42.71% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 583,553 number of insertions = 6,531 mapped reads with insertion percentage = 0.34% number of deletions = 18,641 mapped reads with deletion percentage = 0.98% homopolymer indels = 43.41% >>>>>>> Coverage mean coverageData = 0.035X std coverageData = 0.3294X There is a 3.1% 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% 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 7768750 0.031168427861208818 0.5755027699490624 chr2 243199373 8455533 0.0347679062478504 0.3653784657911348 chr3 198022430 6563798 0.03314673999304018 0.19804117606124905 chr4 191154276 6717356 0.03514101876538718 0.22725350887611145 chr5 180915260 6008033 0.03320910021631122 0.20341887199631717 chr6 171115067 5687818 0.03323972634157342 0.22807958320600252 chr7 159138663 6927406 0.04353062838035782 0.44946430902988693 chr8 146364022 4722084 0.03226260070934645 0.31964071407098577 chr9 141213431 5028295 0.03560776736598093 0.3573376109116267 chr10 135534747 4170176 0.03076831655575378 0.31212528003266055 chr11 135006516 4149955 0.03073892374202146 0.27856061239604885 chr12 133851895 7930199 0.05924607193644887 0.302353920861534 chr13 115169878 4094765 0.035554131610697724 0.20416963507544264 chr14 107349540 3855617 0.03591647435098464 0.23693798869044863 chr15 102531392 2762929 0.026947151951277518 0.18031147495629707 chr16 90354753 3080468 0.034093037695537724 0.22209411783119315 chr17 81195210 3256542 0.0401075629954033 0.22774810753912986 chr18 78077248 3463673 0.04436212966932441 0.6435241308720887 chr19 59128983 1886771 0.031909410652302274 0.4382519135926459 chr20 63025520 3304257 0.052427286597556036 0.25795675009662605 chr21 48129895 1323183 0.027491915367777137 0.2101028943373373 chr22 51304566 1042234 0.020314644119589668 0.153821938647841 chrMT 16571 35270 2.128417114235713 1.8012056056671046 chrX 155270560 5700577 0.036713830361660316 0.2597915768179229 chrY 59373566 313967 0.0052879929765377405 0.1243884495051314