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
A12 F28 I1 R1	227	52.0	1764248	99.3%	1751898	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,640,662	A→G	intergenic (‑87/+24)	hisS ← / ← ispG	histidine‑‑tRNA ligase/(E)‑4‑hydroxy‑3‑methylbut‑2‑enyl‑diphosphate synthase (flavodoxin)

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,640,662	0	A	G	100.0%	168.0 / NA	48	intergenic (‑87/+24)	hisS/ispG	histidine‑‑tRNA ligase/(E)‑4‑hydroxy‑3‑methylbut‑2‑enyl‑diphosphate synthase (flavodoxin)
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (28/20); total (28/20)

GGCAGGTAATCGTTCATGCCGCGAATGGCTTGAATGTTTTTTGCCACGTTTATTCTCTTTCTGAATATAAAAATGAACCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAAGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTCCAGCTGGTCGATCATATCGTTGTTGTCCAGACGG  >  NC_000913/2640529‑2640794

ggcaggTAATCGTTCATGCCGCGAATGGCTTGAATGTTTTTTGCCACGTTTATTCTCTTTCTGAATATAAAAATGAACCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAgg                                                                                                                                <  2:438987/140‑1 (MQ=255)

  caggTAATCGTTCATGCCGCGAATGGCTTGAATGTTTTTTGCCACGTTTATTCTCTTTCTGAATATAAAAATGAACCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGaggcgaggcg                                                                                                                              <  2:419501/140‑1 (MQ=255)

   aggTAATCGTTCATGCCGCGAATGGCTTGAATGTTTTTTGCCACGTTTATTCTCTTTCTGAATATAAAAATGAACCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAAgcgc                                                                                                                             >  1:833436/1‑140 (MQ=255)

     gTAATCGTTCATGCCGCGAATGGCTTGAATGTTTTTTGCCACGTTTATTCTCTTTCTGAATATAAAAATGAACCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCtt                                                                                                                           >  1:153420/1‑140 (MQ=255)

              cATGCCGCGAATGGCTTGAATGTTTTTTGCCACGTTTATTCTCTTTCTGAATATAAAAATGAACCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACg                                                                                                                  >  2:113963/1‑140 (MQ=255)

               aTGCCGCGAATGGCTTGAATGTTTTTTGCCACGTTTATTCTCTTTCTGAATATAAAAATGAACCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGt                                                                                                                 <  2:833436/140‑1 (MQ=255)

                   cgcgAATGGCTTGAATGTTTTTTGCCACGTTTATTCTCTTTCTGAATATAAAAATGAACCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGttatt                                                                                                             >  1:453170/1‑140 (MQ=255)

                         tGGCTTGAATGTTTTTTGCCACGTTTATTCTCTTTCTGAATATAAAAATGAACCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTAttttt                                                                                                       <  1:864948/140‑1 (MQ=255)

                           gCTTGAATGTTTTTTGCCACGTTTATTCTCTTTCTGAATATAAAAATGAACCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCa                                                                                                     <  2:453170/140‑1 (MQ=255)

                            cTTGAATGTTTTTTGCCACGTTTATTCTCTTTCTGAATATAAAAATGAACCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCaa                                                                                                    >  1:553553/1‑140 (MQ=255)

                             ttGAATGTTTTTTGCCACGTTTATTCTCTTTCTGAATATAAAAATGAACCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAAc                                                                                                   >  1:417876/1‑140 (MQ=255)

                              tGAATGTTTTTTGCCACGTTTATTCTCTTTCTGAATATAAAAATGAACCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAAcc                                                                                                  <  2:339641/140‑1 (MQ=255)

                                      ttttGCCACGTTTATTCTCTTTCTGAATATAAAAATGAACCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAAc                                                                                          >  2:842733/1‑140 (MQ=255)

                                              cGTTTATTCTCTTTCTGAATATAAAAATGAACCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTc                                                                                  >  2:578256/1‑140 (MQ=255)

                                               gTTTATTCTCTTTCTGAATATAAAAATGAACCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCg                                                                                 <  2:359133/140‑1 (MQ=255)

                                                           tCTGAATATAAAAATGAACCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTc                                                                     >  2:509540/1‑140 (MQ=255)

                                                               aaTATAAAAATGAACCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGc                                                                 >  1:130345/1‑140 (MQ=255)

                                                                 tataAAAATGAACCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTg                                                               <  2:553553/140‑1 (MQ=255)

                                                                   taAAAATGAACCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGAc                                                             <  1:509540/140‑1 (MQ=255)

                                                                          gAACCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCttt                                                      <  2:521111/140‑1 (MQ=255)

                                                                           aaCCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTc                                                     >  1:647704/1‑140 (MQ=255)

                                                                           aaCCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTc                                                     >  2:251589/1‑140 (MQ=255)

                                                                             cccTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGAc                                                             <  2:401095/130‑1 (MQ=255)

                                                                             cccTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGAc                                                             >  1:401095/1‑130 (MQ=255)

                                                                                 cAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGa                                               <  1:113963/140‑1 (MQ=255)

                                                                                    cGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATg                                            >  2:738409/1‑140 (MQ=255)

                                                                                       ttCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCttt                                                      <  2:416344/127‑1 (MQ=255)

                                                                                       ttCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCttt                                                      >  1:416344/1‑127 (MQ=255)

                                                                                            tCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTc                                    <  2:179427/140‑1 (MQ=255)

                                                                                            tCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTc                                    <  2:652937/140‑1 (MQ=255)

                                                                                            tCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTc                                    >  1:179427/1‑140 (MQ=255)

                                                                                            tCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTc                                    >  1:652937/1‑140 (MQ=255)

                                                                                              aaTGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTCCa                                  >  2:674315/1‑140 (MQ=255)

                                                                                               aTGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTCCAg                                 >  1:441284/1‑140 (MQ=255)

                                                                                                   ttCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTCCAGCTgg                             >  1:738992/1‑140 (MQ=255)

                                                                                                    tCGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTCCAGCTGGt                            <  2:130345/140‑1 (MQ=255)

                                                                                                     cGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTCCAGc                                <  1:61474/135‑1 (MQ=255)

                                                                                                     cGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTCCAGc                                >  2:61474/1‑135 (MQ=255)

                                                                                                     cGGGAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTCCAGCTGGTc                           >  2:485652/1‑140 (MQ=255)

                                                                                                       ggAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTCCAGCTGGTCGa                         <  1:485652/140‑1 (MQ=255)

                                                                                                       ggAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTCCAGCTGGTCGa                         <  2:153420/140‑1 (MQ=255)

                                                                                                        gAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTCCAGCTGGTCGAt                        <  1:674315/140‑1 (MQ=255)

                                                                                                        gAGCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTCCAGCTGGTCGAt                        >  1:78543/1‑140 (MQ=255)

                                                                                                          gCCATGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTCCAGCTGGTCGATCa                      >  1:486189/1‑140 (MQ=255)

                                                                                                             aTGCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTCCAGCTGGTCGATCatat                   >  1:100810/1‑140 (MQ=255)

                                                                                                               gCGGGTTCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTCCAGCTGGTCGATCATATCg                 <  2:156717/140‑1 (MQ=255)

                                                                                                                    ttCAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTCCAGCTGGTCGATCATATCgttgtt            >  2:415548/1‑140 (MQ=255)

                                                                                                                      cAATCATACACGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTCCAGCTGGTCGATCATATCGTtgttgt          >  1:440996/1‑140 (MQ=255)

                                                                                                                             acacGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTCCAGCTGGTCGATCATATCGTTGTTGTCCAGACg   >  2:792200/1‑140 (MQ=255)

                                                                                                                              cacGGGAGGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTCCAGCTGGTCGATCATATCGTTGTTGTCCAGACgg  >  2:784750/1‑140 (MQ=255)

GGCAGGTAATCGTTCATGCCGCGAATGGCTTGAATGTTTTTTGCCACGTTTATTCTCTTTCTGAATATAAAAATGAACCCTCAACGCTTCCCTCAATGTTTCGGGAGCCATGCGGGTTCAATCATACACGGGAAGCGAGGCGCTTCCCATCACGTTATTATTTTTCAACCTGCTGAACGTCAATTCGACGCGCTTCGTCCAGCTGACTGGCTTTCGCACGAATGCGTGCTTCCAGCTGGTCGATCATATCGTTGTTGTCCAGACGG  >  NC_000913/2640529‑2640794

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A