BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524834.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 = 900,620 number of mapped reads = 834,396 (92.65%) number of supplementary alignments = 4,258 (0.47%) number of secondary alignments = 0 number of mapped bases = 48,696,391 bp number of sequenced bases = 48,682,366 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,072 duplication rate = 1.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5084 >>>>>>> ACTG content number of A's = 12,087,094 bp (24.83%) number of C's = 8,729,162 bp (17.93%) number of T's = 15,976,349 bp (32.82%) number of G's = 11,883,305 bp (24.41%) number of N's = 6,456 bp (0.01%) GC percentage = 42.34% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 231,098 number of insertions = 3,053 mapped reads with insertion percentage = 0.36% number of deletions = 8,962 mapped reads with deletion percentage = 1.07% homopolymer indels = 44.04% >>>>>>> Coverage mean coverageData = 0.0157X std coverageData = 0.1776X There is a 1.47% of reference with a coverageData >= 1X There is a 0.07% 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 3995082 0.01602837330543702 0.31136270011298606 chr2 243199373 3169329 0.013031814025277113 0.16725816496027537 chr3 198022430 3545523 0.0179046535283907 0.1397151393569976 chr4 191154276 2670770 0.013971803591775264 0.12962565470453916 chr5 180915260 2976380 0.016451790744462354 0.13442329536594505 chr6 171115067 3231611 0.018885601698651118 0.1518226706343327 chr7 159138663 2246422 0.014116129654802995 0.24144466767094558 chr8 146364022 5320881 0.036353749557387814 0.2531604934970487 chr9 141213431 1999935 0.014162498466594158 0.15734933483337435 chr10 135534747 2430548 0.01793302495337229 0.16787413322671754 chr11 135006516 2221171 0.016452324419659863 0.16349639400278837 chr12 133851895 1967545 0.01469941833845535 0.1273058861502728 chr13 115169878 1247387 0.010830844155274699 0.11032861312987 chr14 107349540 1048506 0.009767214652247228 0.11079818015889542 chr15 102531392 1435096 0.013996649923566824 0.12539828178457266 chr16 90354753 1370520 0.015168211460884632 0.13467418793537342 chr17 81195210 1268177 0.01561886470889108 0.14106992382188116 chr18 78077248 1206066 0.015447086454686518 0.25059486551654736 chr19 59128983 669777 0.011327389141802084 0.19825603145274898 chr20 63025520 1004927 0.015944763327617132 0.1336962750298624 chr21 48129895 719864 0.014956691677802331 0.1323244713842053 chr22 51304566 278040 0.005419400682582521 0.07648050020186167 chrMT 16571 1315 0.07935550057329069 0.28717980721486047 chrX 155270560 2553354 0.016444546860654073 0.1442601441110887 chrY 59373566 118165 0.0019901954347832165 0.05968621558443747