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
A2 F107 I1 R1	11	42.4	1464626	94.8%	1388465	142.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,196,305	C→T	R395C (CGT→TGT)	icd →	isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,196,305	0	C	T	95.7%	119.0 / NA	49	R395C (CGT→TGT)	icd	isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase
Reads supporting (aligned to +/- strand): ref base C (2/0); major base T (25/19); minor base G (1/1); total (28/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

GGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTAGGCTGCTAACGGT  >  NC_000913/1196166‑1196443

gggcAACGTAGATCCTGGTTCTATTATTCTCTCCGCTGAGATGATGTTGCGACACATGAGCTGGACCGACGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTc                                                                                                                                         <  2:254814/140‑1 (MQ=25)

 gACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCt                                                                                                                                        >  1:622018/1‑143 (MQ=255)

 gACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCt                                                                                                                                        >  1:662039/1‑143 (MQ=255)

   cAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTga                                                                                                                                      >  1:286007/1‑143 (MQ=255)

       gTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTgatgga                                                                                                                                  >  2:44198/1‑143 (MQ=255)

               tGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTa                                                                                                                          <  1:216789/143‑1 (MQ=255)

                 gCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACCTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTaaa                                                                                                                        >  2:99644/1‑143 (MQ=255)

                    ctgttctcctctcCGCTGAGATGAGGAAACGCGGCATGGGTTGACCCGCAGCTGCTCACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAActg                                                                                                                     <  2:118117/135‑1 (MQ=18)

                         attCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACGGCTGaa                                                                                                                >  1:660991/1‑143 (MQ=255)

                                ccGCTGAGGTGATGGTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCa                                                                                                         <  2:292864/143‑1 (MQ=255)

                                     gagaTGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGGTGGCGCTAAACTGCTGAAATGGTCAGAGtt                                                                                                    >  1:255048/1‑143 (MQ=255)

                                          gatgCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGCTTGGTg                                                                                               >  1:656024/1‑143 (MQ=255)

                                             tctgcGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcg                                                                                            <  2:163247/142‑1 (MQ=255)

                                               tgcGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTCTGGAAGGCGCAAGCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGGTGGCGCTAAACTGCTGAACGGCTCAGCGTTTGGTCAcgcg                                                                                          >  1:580532/1‑143 (MQ=255)

                                               tgcGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGAATGCTCGATGTAGCTAAACCGCTGAAGTGTCCAGAGTTTGGTGAcgcg                                                                                          >  2:629776/1‑143 (MQ=18)

                                                  gcggcgtGGGTTGGACCGAAGCGGCTGACTTAATGGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGGGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatc                                                                                       <  2:485265/137‑1 (MQ=255)

                                                   ccACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatca                                                                                      >  2:321042/1‑143 (MQ=255)

                                                      caTGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCg                                                                                   >  2:688099/1‑143 (MQ=255)

                                                        ttggttttaCCGTAGCGGCTAACATAACTGCTAATGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTAGGACTGCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaa                                                                                 <  1:296282/135‑1 (MQ=17)

                                                        tgtgTTGGACCGATGCGGTTGACTTAATTGTTGAATGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaa                                                                                 <  1:620634/140‑1 (MQ=18)

                                                           gTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAAc                                                                              >  1:344367/1‑143 (MQ=255)

                                                            ttGGACCGAAGCGGCTGACTTAATGGTTACAGGTATGGAAGGCGCGGTCAACCCGAAAAGCGTAACCTATGACTACGAGGGGCTGATGGAGGGCGCTGAACTGGTGCAATGTTCAGAGGTTGGTGCGTGGGTCATCGAAAACa                                                                             >  2:539007/1‑143 (MQ=255)

                                                                aCCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTa                                                                         >  2:726393/1‑143 (MQ=255)

                                                                 ccGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTaa                                                                        <  1:706122/143‑1 (MQ=255)

                                                                 ccGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTaa                                                                        <  1:44198/143‑1 (MQ=255)

                                                                  cGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAAt                                                                       >  2:351245/1‑143 (MQ=255)

                                                                     aGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGcc                                                                    <  2:267511/143‑1 (MQ=255)

                                                                         gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAg                                                                >  1:680931/1‑143 (MQ=255)

                                                                            gggttgatgggtgaaGGTATGGGAGGCGCATTGAGCGGCAAGACCGTAACCTATGACTTCGAGTGGCTGATGGATGGCACTAAACTGCGGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGttt                                                             <  2:134941/130‑1 (MQ=17)

                                                                               ttAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCGTCGAAAACATGTAATGCCGTAGTTTGtt                                                          >  1:60908/1‑143 (MQ=255)

                                                                               ttAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTCGTTTGtt                                                          >  1:145151/1‑143 (MQ=255)

                                                                               ttAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGtt                                                          >  1:455501/1‑143 (MQ=255)

                                                                                  aTTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTaaa                                                       <  1:446029/143‑1 (MQ=255)

                                                                                       tAAAGGTATGGAAGGCGGAATCAACTCGAAAACCTTAACTTATTTTTTCGAGTTTCTGATTGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATttat                                                  <  1:413746/143‑1 (MQ=18)

                                                                                                      cgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAAc                                   >  1:62407/1‑143 (MQ=255)

                                                                                                       ggaaTCAAGGCGAGAGGCGTATCCGAGGACTTGGAGTGTCGGGTGGAGGGCGCTAAACTGCTGAAATGTTCAGGGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACg                                  <  2:96856/141‑1 (MQ=21)

                                                                                                          aTCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAGTTTATTAACGGGAGCGTAACGCTc                               >  2:408142/1‑143 (MQ=255)

                                                                                                          aTCAACGCGAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGAGAGCGTAACGCTc                               >  2:731476/1‑143 (MQ=255)

                                                                                                                gcgAAAACCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGAAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCgttg                         >  1:305750/1‑143 (MQ=255)

                                                                                                                   aaaaCCGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTACCGTTGttt                      >  2:646872/1‑143 (MQ=255)

                                                                                                                    aaaCCGTAACCTATGACTTCGAGAGGCGGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGtttt                     <  2:286007/143‑1 (MQ=255)

                                                                                                                      ccggTAACCTATGTCTTTGAGTGTCTGATGGATGGCGTTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGtttttt                   <  2:642123/140‑1 (MQ=37)

                                                                                                                       gcGTAACGTATGTCTTCGAGTTGCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTg                  <  2:23826/142‑1 (MQ=25)

                                                                                                                       ccGTAACCTATGACTTCGAGTGTCTGATGGATGGCGCTAAACAGCTGAAATGTTCAGAGTTTGGTGCCGCGATCATCGAAAACATGTAATGCCGTAGGTTGTTAAATTTATTAACGGGGGCGTATAGCACTCCTTGTTTTTTg                  >  2:310463/1‑143 (MQ=21)

                                                                                                                             ccTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTAGgc            <  1:726393/143‑1 (MQ=255)

                                                                                                                              cTATGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGATCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCGGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCGCCCGGTGTTTTTTGTTGGgct           >  1:280606/1‑143 (MQ=25)

                                                                                                                                gtGACTTGGTGTGGCTTATGGATGGCGCTGAACTGCTGAAATGTTCAGTGTTTGGGGTCGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTAGgctgc         <  2:38758/142‑1 (MQ=37)

                                                                                                                                aTGACTTCGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTAGgctgc         <  1:463804/143‑1 (MQ=255)

                                                                                                                                       cGAGTGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAAAGCTCCCGTTGTTTTTTGTTAGGCTGCTAACGGt  >  1:195473/1‑143 (MQ=255)

GGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGTTTTTTGTTAGGCTGCTAACGGT  >  NC_000913/1196166‑1196443

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A