BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716585.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 = 1,972,199 number of mapped reads = 950,018 (48.17%) number of supplementary alignments = 3,322 (0.17%) number of secondary alignments = 0 number of mapped bases = 53,406,214 bp number of sequenced bases = 53,390,637 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,297 duplication rate = 1.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.1011 >>>>>>> ACTG content number of A's = 12,868,548 bp (24.1%) number of C's = 10,838,092 bp (20.3%) number of T's = 16,315,077 bp (30.56%) number of G's = 13,368,449 bp (25.04%) number of N's = 471 bp (0%) GC percentage = 45.34% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 279,845 number of insertions = 3,178 mapped reads with insertion percentage = 0.33% number of deletions = 9,800 mapped reads with deletion percentage = 1.03% homopolymer indels = 40.35% >>>>>>> Coverage mean coverageData = 0.0173X std coverageData = 0.1704X There is a 1.6% of reference with a coverageData >= 1X There is a 0.09% 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 4505170 0.018074859681091827 0.19813832760635633 chr2 243199373 4140448 0.01702491231340469 0.25436404092172843 chr3 198022430 3075131 0.015529205454149816 0.13469262504388801 chr4 191154276 3215551 0.016821758148899583 0.14129856892150972 chr5 180915260 3045232 0.016832366711354255 0.13675732754195322 chr6 171115067 2843447 0.016617163233206108 0.15510029519015958 chr7 159138663 3058095 0.019216543248198586 0.2196541255256916 chr8 146364022 2735520 0.018689838955095125 0.1611005946356411 chr9 141213431 1784108 0.01263412401614971 0.13393977960402936 chr10 135534747 2344711 0.01729970396447488 0.195915557182795 chr11 135006516 1878299 0.013912654408473144 0.1470067675581208 chr12 133851895 2671307 0.019957184767537283 0.1524192463079479 chr13 115169878 1601074 0.013901846800601803 0.1257915825742683 chr14 107349540 1779267 0.016574519089695216 0.14094772308524162 chr15 102531392 1974368 0.019256229350714364 0.15119397093793335 chr16 90354753 1904543 0.021078503750654932 0.1625041057232023 chr17 81195210 2436365 0.030006265147907125 0.1904573128426054 chr18 78077248 992863 0.012716419000833637 0.18464413879813474 chr19 59128983 1467158 0.024812840092311415 0.2048352826100123 chr20 63025520 1738128 0.02757816198898478 0.18162974408353114 chr21 48129895 648488 0.01347370485640993 0.13162895060535537 chr22 51304566 516645 0.010070156328775884 0.10619885477097091 chrMT 16571 18065 1.0901575040733813 1.177547923799096 chrX 155270560 2875581 0.018519808262429143 0.15106545689183187 chrY 59373566 156650 0.0026383795105047255 0.07770895802340469