Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A4 F27 I0 R1	185	118.8	2757226	85.6%	2360185	223.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	4,452,852	A→G	30.3%	G94G (GGA→GGG)	ytfT →	putative sugar ABC transporter permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,452,852	0	A	G	30.3%	46.1 / 2.3	30	G94G (GGA→GGG)	ytfT	putative sugar ABC transporter permease
Reads supporting (aligned to +/- strand): ref base A (6/14); new base G (6/4); total (12/18)
Fisher's exact test for biased strand distribution p-value = 1.39e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCAGCTGGTAGCACTATTGCTGGTGCTGCTGGTCGATAGCCTGGTAGCCCCGCATTTCTGGCAGGTGGTGCTTCAGGATGGGCGTTTG‑TTCGGTAGCCCCATAGACATTCTTAACCGTGCAGCTCCCGTTGCGTTACTGGCGATTGGCATGACGCTGGTGATCGCCACCGGTGGGATTGATCTCTCCGTAGGGGCGGTGATGGCTATCGCCGGAGCCACAACGGCTGCGATGA‑CGGT‑CGCGGGATTCAGCCTGCCGATTGTTTTGTTAAGCGCCCTGGGCACCGGCATCCTGGCGGGATTGTGGAACGGCATACTGGTAGCGATCCTCAAAATTCAGCCGTTTGTCGCCACTCTGATCCTGATG‑GTCGCCGGGCGCGGCGTGGCGCAACTGATCACCGCCGGGCAGATCGTCACGTTTAACTCGCCGGATCTCTCATGGTTCGGCAG  >  NC_000913/4452639‑4453085

gCAGCTGGTAGCACTATTGCTGGTGCTGCTGGTCGATAGCCTGGTAGCCCCGCATTTCTGGCAGGTGGTGCTTCAGGATGGGCGTTTG‑TTCGGTAGCCCCATAGACATTCTTAACCGTGCAGCTCCCGTTGCGTTACTGGCGATTGGCATGACGCTGGTGATCGCCACCGGTGGGATTGATCTCTCCGTAGGGGCGGTGATGGCTATCGCCGGAGCCACAACGGCTGCGATGA‑CGGT‑cg                                                                                                                                                                                                                   <  1:732110/239‑1 (MQ=255)

gCAGCTGGTAGCACTATTGCTGGTGCTGCTGGTCGATAGCCTGGTAGCCCCGCATTTCTGGCAGGTGGTGCTTCAGGATGGGCGTTTG‑TTCGGTAGCCCCATAGACATTCTTAACCGTGCAGCTCCCGTTGCGTTACTGGCGATTGGCATGACGCTGGTGATCGCCACCGGTGGGATTGATCTCTCCGTAGGGGCGGTGATGGCTATCGCCGGAGCCACAACGGCTGCGATGA‑CGGT‑cg                                                                                                                                                                                                                   <  1:164789/239‑1 (MQ=255)

                        gctgctGGTCGATAGCCTGGTAGCCCCGCATTTCTGGCAGGTGGTGCTTCAGGATGGGCGTTTG‑TTCGGTAGCCCCATAGACATTCTTAACCGTGCAGCTCCCGTTGCGTTACTGGCGATTGGCATGACGCTGGTGATCGCCACCGGTGGGATTGATCTCTCCGTAGGGGCGGTGGTGGGTATTTCCCGGACGCCAACGGCTTCGGATA‑CGGT‑CGCCGGGCTAAGCCTGCCGGttgtgt                                                                                                                                                                                           >  1:296375/1‑237 (MQ=255)

                        gctgctGGTCGATAGCCTGGTAGCCCCGCATTTCTGGCAGGTGGTGCTTCAGGATGGGCGTTTG‑TTCGGTAGCCCCATAGACATTCTTAACCGTGCAGCTCCCGTTGCGTTACTGGCGATTGGCATGACGCTGGTGATCGCCACCGGTGGGATTGATCTCTCCGTAGGGGCGGTGAAGGATATCGCCGGAGCCACAACGGCTGCGGGTA‑CGGT‑CGCGGGGTTAGGCGTGCCGAtttttt                                                                                                                                                                                           >  1:983888/1‑239 (MQ=255)

                        gctgctGGTCGATAGCCTGGTAGCCCCGCATTTCTGGCAGGTGGTGCTTCAGGATGGGCGTTTG‑TTCGGTAGCCCCATAGACATTCTTAACCGTGCAGCTCCCGTTGCGTTACTGGCGATTGGCATGACGCTGGTGATCGCCACCGGTGGGATTGATCTCTCCGTAGGGGCGGGGATGGCCATCGCCGGGGCCCCAACGGCTCCGGTGA‑CGGT‑CGCGGGGTTCCGCCTGCCCAttgttt                                                                                                                                                                                           >  1:486295/1‑239 (MQ=255)

                                         tGGTAGCCCCGCATTTCTGGCAGGTGGTGCTTCAGGATGGGCGTTTG‑TTCGGTAGCCCCATAGACATTCTTAACCGTGCAGCTCCCGTTGCGTTACTGGCGATTGGCATGACGCTGGTGATCGCCACCGGTGGGATTGATCTCTCCGTAGGGGCGGTGATGGCTATCGCCGGAGCCACAACGGCTCGGATGA‑CGGT‑CCCGGGGTTTAGCCTGCCGGTTGTTTTGTTTAGGGCCCTggg                                                                                                                                                                           >  1:830271/1‑238 (MQ=255)

                                         tGGTAGCCCCGCATTTCTGGCAGGAGGTGCTTCAGGATGGGCGTTTG‑TTCGGTAGCCCCATAGACATTCTTAACCGTGCAGCTCCCGTTGCGTTACTGGCGATTGGCATGACGCTGGTGATCGCCACCGGTGGGATTGATCTCTCCGTAGGGGGGGGGGTGGCTATTGCCGGAGCCCAAACAGCTTGGCGTA‑CGGTGCCGGGGATTC‑GCCTGCCCATTGTTTTGTTTAGCGccacggg                                                                                                                                                                           >  1:998862/1‑233 (MQ=255)

                                              gCCCCGCATTTCTGGCAGGTGGTGCTTCAGGATGGGCGTTTG‑TTCGGTAGCCCCATAGACATTCTTAACCGTGCAGCTCCCGTTGCGTTACTGGCGATTGGCATGACGCTGGTGATCGCCACCGGTGGGATTGATCTCTCCGTAGGGGCGGTGATGGCGTTCGCCGGAGCCACAACGGCCGCGATGA‑CGGT‑GCCGGGGTTTACGCTCCCGATTGTTTTGTTAACAGCCCTGGGGAccc                                                                                                                                                                      >  1:880005/1‑237 (MQ=255)

                                                cccGCATTTCTGGCAGGTGGTGCTTCAGGATGGGCGTTTG‑TTCGGTAGCCCCATAGACATTCTTAACCGTGCAGCTCCCGTTGCGTTACTGGCGATTGGCATGACGCTGGTGATCGCCACCGGTGGGATTGATCTCTCCGTAGGGGCGGTGATGGCTATCGCCGGGGCCACAAAGGCCGCGGTTA‑CGGT‑CGCGGGGTTCACCCTGCCGGATGTTTTGTTAAGCGCCCTGGGCACCGGc                                                                                                                                                                    >  1:1002792/1‑238 (MQ=255)

                                                 ccGCATTTCTGGCAGGTGGTGCTTCAGGATGGGCGTTTG‑TTCGGTAGCCCCATAGACATTCTTAACCGTGCAGCTCCCGTTGCGTTACTGGCGATTGGCATGACGCTGGTGATCGCCACCGGTGGGATTGATCTCTCCGTAGGGGCGGTGATGGCTATCGCCGGGGGCCCAACGGCTGCGGTGA‑CGGT‑CGCGGGGTTCAGCCTGCCGCTTGTTTTGTTTACTGCCCCGGGGACCGGcc                                                                                                                                                                   >  1:14957/1‑237 (MQ=255)

                                                  cGCATTTCTGGCAGGTGGTGCTTCAGGATGGGCGTTTG‑TTCGGTAGCCCCATAGACATTCTTAACCGTGCAGCTCCCGTTGCGTTACTGGCGATTGGCATGACGCTGGTGATCGCCACCGGTGGGATTGATCTCGCCGTAGGGGCGGGGATGGCTTTCGCCGGGGCCCCAACGGGTGGCAGGAGGGGG‑CGGGGGATCACGGCGCCCGCTTGTTTTGTTAACCGCCCTGGCCCCCGGccc                                                                                                                                                                  >  2:882603/1‑237 (MQ=255)

                                                         ttGGCGGGGGGTTCTTCGGGTGTGGGGTTTG‑TTCGGTCGCCCCATAGACATTTTTAACCGGGCAGCCCCCGTTGCGTTACTGGCGATTGGCATGACGCTGGTGATCGCCACCGGTGGGATTGATCTCTCCGTAGGGGCGGTGATGGCTATCGCCGGAGCCACAACGGCTGCGATGA‑CGGT‑CGCGGGATTCAGCCTGCCGATTGTTTTGTTAAGCGCCCTGGGCACCGGCATCCTGGCgg                                                                                                                                                          <  2:486295/238‑1 (MQ=255)

                                                                 tggtgTCTCGGGGTGGGGGTTTT‑GTTGGTGGCCCTATAGACATTCGTGACCGGGCCGCCCTCGTTGGTGTACTGGCGATTGGCATGACGTTGGGGATCGCGCCCGGTGGGATTGATCTCTCCGTAGGGGCGGTGATGGCTATCGCCGGGGCCACAACGGCTGCGATGA‑CGGT‑CGCGGGATTCAGCCTGCCGATTGTTTTGTTAAGCGCCCTGGGCACCGGCATCCTGGCGGGATtgtg                                                                                                                                                   <  2:14957/238‑1 (MQ=255)

                                                                    gtgtttcggctGGGGGTTTGTTTCGGTGGCCCCATGCGAATGCTTAACCGGGCCGCCCCCGTGGCGTTACGGGCAATTGGCATGACGCTGGTGATCCCCACCGGTGGGATTGATCTCTCCGTAGGGGCGGTGATGGCTATCGCCGGAGCCACAACGGCTGCGATGA‑CGGT‑CGCGGGATTCAGCCTGCCGATTGTTTTGTTAAGCGCCCTGGGCACCGGCATCCTGGCGGGATTGTGGaa                                                                                                                                                <  2:806899/229‑1 (MQ=255)

                                                                        ttaGGATGGGCGTTGG‑TTCGGTAGCCCCATAGACATTCTTAACCGGGCAGCTCCCGTTGCGTTACTGGCGATTGGCATGACGCTGGTGATCGCCACCGGGGGGATTGATCTCTCCGTAGGGGCGGTGATGGCTATCGCCGGAGCCACAACGGCTGCGATGA‑CGGT‑CGCGGGATTCAGCCTGCCGATTGTTTTGTTAAGCGCCCTGGGCACCGGCATCCTGGCGGGATTGTGGAACGGCa                                                                                                                                           <  1:240455/237‑1 (MQ=255)

                                                                                                           cttcttcCCCGTGCCCCCCCCGTTGCGTTACTGGCGGTTGGCAGGCGGCTGGTGAGCGCCGCCGGTGGGATTGATCTCTCCGTAGGGGCGGTGATGGCTATCGCCGGAGCCACAACGGCTGCGATGA‑CGGT‑CGCGGGATTCAGCCTGCCGATTGTTTTGTTAAGCGCCCTGGGCACCGGCATCCTGGCGGGATTGTGGAACGGCATACTGGTAGCGATCCTCAAAATTCAGCCGTTTGt                                                                                                         <  2:618828/238‑1 (MQ=255)

                                                                                                             tCTTAGCCTTGCTGCTCCGGTTGCGTTACTGGAGTTTGGCATGGCGCTGGTGATCGCCTCCGGTGGGATTGATCTCTCCGTTGGGGCGGTGATGGCTATCGCCGGAGCCACAACGGCTGCGATGA‑CGGT‑CGCGGGATTCAGCCTGCCGATTGTTTTGTTAAGCGCCCTGGGCACCGGCATCCTGGCGGGATTGTGGAACGGCATACTGGTAGCGATCCTCAAAATTCAGCCGTTTGTCg                                                                                                       <  1:107388/239‑1 (MQ=255)

                                                                                                              cTTAACCGTGCAGCTCCCGTTGCGTTACTGGCGATTGGCATGACGCTGGTGATCGCCACCGGTGGGATTGATCTCTCCGTAGGGGCGGTGATGGCTATCGCCGGAGCCACAACGGCTGCGATGA‑CGGT‑CGCGGGATTCAGCCTGCCGATTGTTTTGTTAAGCGCCCTGGGCACCGGCATCCTGGCGGGATTGTGGAACGGCATACTGGTAGCGATCCTCAAAATTCAGCCGTTTGTCGc                                                                                                      <  1:523193/239‑1 (MQ=255)

                                                                                                                tAACCGTGGAGCTCCCGTTGGGTTACTGGCGATTGGCCTGGCGCTGGTGATCGCCCCCGGTGGGATTGATCTCTCCGTAGGGGCGGTGATGGCTATCGCCGGAGCCACAACGGCTGCGATGA‑CGGT‑CGCGGGATTCAGCCTGCCGATTGTTTTGTTAAGCGCCCTGGGCACCGGCATCCTGGCGGGATTGTGGAACGGCATACTGGTAGCGATCCTCAAAATTCAGCCGTTTGTCGCCa                                                                                                    <  1:1300438/239‑1 (MQ=255)

                                                                                                                                                 tgggggggcGCTGGTGAGCGCTACGGGGGGGATTGTTCTCCCCGGCGGGGCGGGGATGGCTATCGCCGTGGCCACAACGGCTGCGATGA‑CGGT‑CGCGGGATTCAGCCTGCCGATTGTTTTGTTAAGCGCCCTGGGCACCGGCATCCTGGCGGGATTGTGGAACGGCATACTGGTAGCGATCCTCAAAATTCAGCCGTTTGTCGCCACTCTGATCCTGATG‑GTCGCCGGGCGCGGCGTgg                                                                  <  2:969109/231‑1 (MQ=255)

                                                                                                                                                   gcctggcgcgGGTGTTCCCCACCGGTGGGGTTGACCTCTCCGGTGGGGCGGTGATGGCTACCGCCGGAGCCACAACGGCTGGGATGA‑CGGT‑CGCGGGATTCAGCCTGCCGATTGTTTTGTTAAGCGCCCTGGGCACCGGCATCCTGGCGGGATTGTGGAACGGCATACTGGTAGCGATCCTCAAAATTCAGCCGTTTGTCGCCACTCTGATCCTGATG‑GTCGCCGGGCGCGGCGTGgcg                                                                <  2:834312/233‑1 (MQ=255)

                                                                                                                                                       gcggCTGGTGATCGCCACCGGTGGGATTGATCTCTCCGTAGGGGCGGTGATGGCTAGCGCCGGAGCCACAACGGCTGCGATGA‑CGGT‑CGCGGGATTCAGCCTGCCGATTGTTTTGTTAAGCGCCCTGGGCACCGGCATCCTGGCGGGATTGTGGAACGGCATACTGGTAGCGATCCTCAAAATTCAGCCGTTTGTCGCCACTCTGATCCTGATG‑GTCGCCGGGCGCGGCGTGGCGCaa                                                             <  1:866157/235‑1 (MQ=255)

                                                                                                                                                                             gggATTGATCTCTCCGTAGGGGCGGAGCAGGCTATCGCCCGGACCCCAACGGCCGCGATGA‑CGGT‑CGCGGGATTCAGCCTGCCGGTTGTTTTGTTAAGCGCCCCGGGCACCGGCATCCTGGCGGGGGTGTGGGAAGGGAGACTGGTAGGGAGACCCAAAATTTAGCCGTTTGTCGCCCCTCCTGTTCTGATGTGGCGCCGGG‑GCGGGGGGGGGGCACGCGTCACCGCCggggcagggg                                       >  2:911769/1‑231 (MQ=255)

                                                                                                                                                                                                 gggggggagggCTATCGCGGGAGCCACAACGGTTGCGATGA‑CGGT‑CGCGGGATTCAGCCTGCCGATTGTTTTGTTAAGCGCCCTGGGCACCGGCATCCTGGCGGGATTGTGGAACGGCATACTGGTAGCGATCCTCAAAATTCAGCCGTTTGTCGCCACTCTGATCCTGATG‑GTCGCCGGGCGCGGCGTGGCGCAACTGATCACCGCCGGGCAGATCGTCACGTTTAACTCGCCGGAt                   <  1:804363/229‑1 (MQ=255)

                                                                                                                                                                                                  ggggggATGGCTAGCGGCGGGGCCCAAACGGCTGGGATGA‑CGGT‑CGGGGGATTCAGCCTGGCGATTGTTTTGTTAAGCGCCCTGGGCACCGGCATCCTGGCGGGATTGTGGAACGGCATACTGGTAGCGATCCTCAAAATTCAGCCGTTTGTCGCCACTCTGATCCTGATG‑GTCGCCGGGCGCGGCGTGGCGCAACTGATCACCGCCGGGCAGATCGTCACGTTTAACTCGCCGGAtc                  <  1:1254938/233‑1 (MQ=255)

                                                                                                                                                                                                            gctccGCCGGGGCCACAACGGGTGGGGTGA‑CGGT‑CGGGGGATTACGCCTGCCGGTTGTTTTGTTAAGCGCCCTGGGCACCGGCATCCTGGCGGGATTGTGGAACGGCATACTGGTAGCGATCCTCAAAATTCAGCCGTTTGTCGCCACTCTGATCCTGATG‑GTCGCCGGGCGCGGCGTGGCGCAACTGATCACCGCCGGGCAGATCGTCACGTTTAACTCGCCGGATCTCTCATGGtt        <  2:880005/234‑1 (MQ=255)

                                                                                                                                                                                                                cGCCGGAGCCACAACGGCTGGGATGA‑CGGT‑CGCGGGATTCAGCCTGCCGATTGTTTTGTTAAGCGCCCTGGGCACCGGCATCCTGGCGGGATTGTGGAACGGCATACTGGTAGCGATCCTCAAAATTCAGCCGTTTGTCGCCACTCTGATCCTGATG‑GTCGCCGGGCGCGGCGTGGCGCAACTGATCACCGCCGGGCAGATCGTCACGTTTAACTCGCCGGATCTCTCATGGTTCGGCa   <  1:1263133/239‑1 (MQ=255)

                                                                                                                                                                                                                cGCCGGAGCCACAACGGCTGCGATGA‑CGGT‑CGCGGGATTCAGCCTGCCGATTGTTTTGTTAAGCGCCCTGGGCACCGGCATCCTGGCGGGATTGTGGAACGGCATACTGGTAGCGATCCTCAAAATTCAGCCGTTTGTCGCCACTCTGATCCTGATG‑GTCGCCGGGCGCGGCGTGGCGCAACTGATCCCCGCCGGGCAGACCGTCCCGTTTAACCCGCCGGATTCTTCATGGTTCgccc   >  1:767622/1‑236 (MQ=255)

                                                                                                                                                                                                                cGCCGGAGCCACAACGGCTGCGATGA‑CGGT‑CGCGGGATTCAGCCTGCCGATTGTTTTGTTAAGCGCCCTGGGCACCGGCATCCTGGCGGGATTGTGGAACGGCATACTGGTAGCGATCCTCAAAATTCAGCCGTTTGTCGCCACTCTGATCCTGATG‑GTCGCCGGGCGCGGCGTGGCGCAACTGATCACCGCCGGGCAGATCGTCACGTTTAACTCGCCGGATCTCTCATGGTTCGGCa   >  1:887306/1‑239 (MQ=255)

                                                                                                                                                                                                                 gacGGAGCCACACCGGTTGCGATGA‑CGGC‑CGCGGGATTCAGCCTGCCGATTGTCTTGTTAATCGTCCTTGGCACCGGCATCCGGGCGGGATTGTGGAACGGCATACTGGTAGCGATCCTCAAAATTCAGCCGTTTGTCGCCACTCTGATCCTGATG‑GTCGCCGGGCGCGGCGTGGCGCAACTGATCACCGCCGGGCAGATCGTCACGTTTAACTCGCCGGATCTCTCATGGTTCGGCAg  <  1:25929/237‑1 (MQ=255)

GCAGCTGGTAGCACTATTGCTGGTGCTGCTGGTCGATAGCCTGGTAGCCCCGCATTTCTGGCAGGTGGTGCTTCAGGATGGGCGTTTG‑TTCGGTAGCCCCATAGACATTCTTAACCGTGCAGCTCCCGTTGCGTTACTGGCGATTGGCATGACGCTGGTGATCGCCACCGGTGGGATTGATCTCTCCGTAGGGGCGGTGATGGCTATCGCCGGAGCCACAACGGCTGCGATGA‑CGGT‑CGCGGGATTCAGCCTGCCGATTGTTTTGTTAAGCGCCCTGGGCACCGGCATCCTGGCGGGATTGTGGAACGGCATACTGGTAGCGATCCTCAAAATTCAGCCGTTTGTCGCCACTCTGATCCTGATG‑GTCGCCGGGCGCGGCGTGGCGCAACTGATCACCGCCGGGCAGATCGTCACGTTTAACTCGCCGGATCTCTCATGGTTCGGCAG  >  NC_000913/4452639‑4453085

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 25 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A