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
A3 F50 I2 R1	193	39.9	1341687	91.8%	1231668	149.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,753,413	A→G	Y229Y (TAT→TAC)	yiaV ←	signal‑anchored membrane fusion protein (MFP) component of efflux pump

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,753,413	0	A	G	97.1%	115.0 / ‑3.4	35	Y229Y (TAT→TAC)	yiaV	signal‑anchored membrane fusion protein (MFP) component of efflux pump
Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (19/15); total (19/16)
Fisher's exact test for biased strand distribution p-value = 4.57e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.98e-01

GTCGCCAGGAGCCAGTCGCAGCAAGGAGTTCTGACGGAACTGCGCCACGATTTGTCGTTTCTGATCGGGTATAAACACCATCACCGGACGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACATAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGCTTTCAGGCTGGCGATTTGAGAATGTTCACCCAACACCAGGCTATCCAGCTGGCTCTGGATCTGTTTTTGTTCCGCCGCCG  >  NC_000913/3753272‑3753558

gtcgCCAGGAGCCAGTCGCAGCAAGGAGTTCTGACGGAACTGCGCCACGATTTGTCGTTTCTGATCGGGTATAAACACCATCACCGGACGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCg                                                                                                                                          >  1:110060/1‑151 (MQ=255)

      aGGAGCCAGTCGCAGCAAGGAGTTCTGACGGAACTGCGCCACGATTTGTCGTTTCTGATCGGGTATAAACACCATCACCGGACGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCGgc                                                                                                                                    >  2:661145/1‑151 (MQ=255)

       ggAGCCAGTCGCAGCAAGGAGTTCTGACGGAACTGCGCCACGATTTGTCGTTTCTGATCGGGTATAAACACCATCACCGGACGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACATAACCATCGCTCGgcg                                                                                                                                   <  1:507816/151‑1 (MQ=255)

                   agcaAGGAGTTCTGACGGAACTGCGCCACGATTTGTCGTTTCTGATCGGGTATAAACACCATCACCGGACGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCg                                                                                                                       >  1:287995/1‑151 (MQ=255)

                          aGTTCTGACGGAACTGCGCCACGATTTGTCGTTTCTGATCGGGTATAAACACCATCACCGGACGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTc                                                                                                                <  2:429545/151‑1 (MQ=255)

                            ttCTGACGGAACTGCGCCACGATTTGTCGTTTCTGATCGGGTATAAACACCATCACCGGACGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCa                                                                                                               >  2:648337/1‑150 (MQ=255)

                              cTGACGGAACTGCGCCACGATTTGTCGTTTCTGATCGCGTATAAACACCATCACCGGACGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAgg                                                                                                            >  1:598042/1‑151 (MQ=255)

                                    gAACTGCGCCACGATTTGTCGTTTCTGATCGGGTATAAACACCATCACCGGACGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTatat                                                                                                      <  1:500651/151‑1 (MQ=255)

                                        tGCGCCACGATTTGTCGTTTCTGATCGGGTATAAACACCATCACCGGACGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTg                                                                                                  >  1:532542/1‑151 (MQ=255)

                                          cgcCACGATTTGTCGTTTCTGATCGGGTATAAACACCATCACCGGACGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCt                                                                                                >  2:430505/1‑151 (MQ=255)

                                               cGATTTGTCGTTTCTGATCGGGTATAAACACCATCACCGGACGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCcgc                                                                                           <  1:565366/151‑1 (MQ=255)

                                                       cGTTTCTGATCGGGTATAAACACCATCACCGGACGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCtgtg                                                                                   <  1:451826/151‑1 (MQ=255)

                                                        gTTTCTGATCGGGTATAAACACCATCACCGGACGTAGCGGCAGCGACGCGGCATAGGTACCCGGACAAATCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGc                                                                                  >  2:101819/1‑151 (MQ=255)

                                                         tttCTGATCGGGTATAAACACCATCCCCGGACGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTACCCATCGCTCGGCGCACGCACTATCGTCGGCTCAAGGTTATATTTTGCTTCCGCGAGCtgt                                                                                    <  1:430697/148‑1 (MQ=255)

                                                          ttCTGATCGGGTATAAACACCATCACCGGACGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGCtt                                                                                >  2:88168/1‑151 (MQ=255)

                                                                   ggTATAAACACCATCACCGGACGTATCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTATCCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGCTTTCAGGCTg                                                                        <  1:596535/150‑1 (MQ=255)

                                                                     tataAACACCATCACCGGACGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCAGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGCTTTCAGGCTGGCg                                                                     >  1:340896/1‑151 (MQ=255)

                                                                         aaCACCATCACCGGACGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGCTTTCAGGCTGGCGAttt                                                                 >  1:59286/1‑151 (MQ=255)

                                                                             ccATCACCGGACGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGCTTTCAGGCTGGCGATTTg                                                                >  2:330737/1‑148 (MQ=255)

                                                                               aTCACCGGACGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGCTTTCAGGCTGGCGATTTGAGAAt                                                           <  1:148939/151‑1 (MQ=255)

                                                                                 cACCGGACGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATAAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGCTTTCAGGCTGGCGATTTGAGAATGt                                                         <  2:17011/151‑1 (MQ=255)

                                                                                      gACGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGCTTTCAGGCTGGCGATTTGAGAATGTTCAcc                                                    >  2:379047/1‑151 (MQ=255)

                                                                                        cGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGCTTTCAGGCTGGCGATTTGAGAATGTTCACCCa                                                  <  1:644968/151‑1 (MQ=255)

                                                                                        cGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGCTTTCAGGCTGGCGATTTGAGAATGTTCACCCa                                                  <  1:231481/151‑1 (MQ=255)

                                                                                           aGCGGCAGCGACGCAGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGCTTTCAGGCTGGCGATTTGAGAATGTTCACCCAaca                                               <  2:367570/151‑1 (MQ=255)

                                                                                            gCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGCTTTCAGGCTGGCGATTTGAGAATGTTCACCCAacac                                              <  2:58413/151‑1 (MQ=255)

                                                                                             cGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGCTTTCAGGCTGGCGATTTGAGAATGTTCACCCAACAcc                                             >  1:485977/1‑151 (MQ=255)

                                                                                                  gCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGCTTTCAGGCTGGCGATTTGAGAATGTTCACCCAACACCAGGCt                                        <  2:379985/151‑1 (MQ=255)

                                                                                                       gcgGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGCTTTCAGGCTGGCGATTTGAGAATGTTCACCCAACACCAGGCTATcc                                    >  2:571724/1‑150 (MQ=255)

                                                                                                       gcgGCATAGGTACCCGGACGAATCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGCTTTCAGGCTGGCGATTTGAGAATGTTCACCCAACACCAGGCTATCCa                                   <  1:525254/151‑1 (MQ=255)

                                                                                                                             tCAGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGCTTTCAGGCTGGCGATTTGAGAATGTTCACCCAACACCAGGCTATCCAGCTGGCTCTGGATCTGTTTTTg             >  2:34875/1‑151 (MQ=255)

                                                                                                                               aGTACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGCTTTCAGGCTGGCGATTTGAGAATGTTCACCCAACACCAGGCTATCCAGCTGGCTCTGGATCTGTTTTTGtt           >  2:86024/1‑151 (MQ=255)

                                                                                                                                 tACCTGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGCTTTCAGGCTGGCGATTTGAGAATGTTCACCCAACACCAGGCTATCCAGCTGGCTCTGGATCTGTTTTTGTTcc         >  2:484340/1‑151 (MQ=255)

                                                                                                                                     tGGGTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGCTTTCAGGCTGGCGATTTGAGAATGTTCACCCAACACCAGGCTATCCAGCTGGCTCTGGATCTGTTTTTGTTccgccg     >  1:291156/1‑151 (MQ=255)

                                                                                                                                        gTCACGTAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGCTTTCAGGCTGGCGATTTGAGAATGTTCACCCAACACCAGGCTATCCAGCTGGCTCTGGATCTGTTTTTGTTccgccgccg  <  1:609303/151‑1 (MQ=255)

GTCGCCAGGAGCCAGTCGCAGCAAGGAGTTCTGACGGAACTGCGCCACGATTTGTCGTTTCTGATCGGGTATAAACACCATCACCGGACGTAGCGGCAGCGACGCGGCATAGGTACCCGGACGAATCAGTACCTGGGTCACATAACCATCGCTCGGCGCACGCACTATCGTCTGCTCAAGGTTATATTTTGCTTCCGCGAGCTGTGCTTTCAGGCTGGCGATTTGAGAATGTTCACCCAACACCAGGCTATCCAGCTGGCTCTGGATCTGTTTTTGTTCCGCCGCCG  >  NC_000913/3753272‑3753558

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A