BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716191.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 = 849,649 number of mapped reads = 803,056 (94.52%) number of supplementary alignments = 17,166 (2.02%) number of secondary alignments = 0 number of mapped bases = 62,713,844 bp number of sequenced bases = 62,689,172 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,319 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.785 >>>>>>> ACTG content number of A's = 15,719,577 bp (25.08%) number of C's = 13,432,994 bp (21.43%) number of T's = 18,132,920 bp (28.93%) number of G's = 15,401,399 bp (24.57%) number of N's = 2,282 bp (0%) GC percentage = 46% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 399,607 number of insertions = 4,883 mapped reads with insertion percentage = 0.6% number of deletions = 11,950 mapped reads with deletion percentage = 1.46% homopolymer indels = 39.26% >>>>>>> Coverage mean coverageData = 0.0203X std coverageData = 0.1951X There is a 1.81% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% 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 6966231 0.027948700677459897 0.33658864229203456 chr2 243199373 5823921 0.02394710532415723 0.20876906387792837 chr3 198022430 4007806 0.020239151696098266 0.15528174061458047 chr4 191154276 3031540 0.015859127315572055 0.17025277344252354 chr5 180915260 3189932 0.01763218868325425 0.14542155415077995 chr6 171115067 3843512 0.022461563831781103 0.16853750760323988 chr7 159138663 3880036 0.02438147918837297 0.23904545771456315 chr8 146364022 3889451 0.026573818803640147 0.21215750178271744 chr9 141213431 1882121 0.013328201054756612 0.14348386691031717 chr10 135534747 3201262 0.023619492940802848 0.23926177450375546 chr11 135006516 1939817 0.014368321303839882 0.15452347314992343 chr12 133851895 2375701 0.01774872892161893 0.14613745445715268 chr13 115169878 1150797 0.009992170001256752 0.10778764637946786 chr14 107349540 1250895 0.011652541780803159 0.1202214167949549 chr15 102531392 1320412 0.012878124194393069 0.12288029527485202 chr16 90354753 1910587 0.02114539563845634 0.16336075547654402 chr17 81195210 1616869 0.019913354494680166 0.16251906861638718 chr18 78077248 1879747 0.02407547714796505 0.21114948313921958 chr19 59128983 1604766 0.027140091349110468 0.2658776168299503 chr20 63025520 1698012 0.02694165791888746 0.18428161575117247 chr21 48129895 986939 0.020505737650165244 0.1748131325188318 chr22 51304566 1042124 0.020312500060910756 0.16021501294242008 chrMT 16571 22216 1.3406553617765977 1.5787177171421498 chrX 155270560 4003417 0.02578349044403524 0.18044667045682597 chrY 59373566 195733 0.0032966354084240116 0.11656992093609343