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
A13 F191 I0 R1	49	68.0	1456600	97.2%	1415815	140.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,502,141	C→A	100%	A222D (GCC→GAC)	USA300HOU_2364 →	AraC transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,502,141	0	C	A	100.0%	143.1 / ‑6.5	52	A222D (GCC→GAC)	USA300HOU_2364	AraC transcriptional regulator
Reads supporting (aligned to +/- strand): ref base C (1/0); new base A (33/18); total (34/18)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TCATATTGTTCTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGCCGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTCCAACAAGATAACGTATCACA  >  CP000730/2502008‑2502276

tCATATTGTTCTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGttt                                                                                                                                   <  2:568446/140‑1 (MQ=255)

 cATATTGTTCTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGtttt                                                                                                                                  >  1:78181/1‑140 (MQ=255)

  atatTGTTCTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAGGTATTAAACTTGTTGACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTa                                                                                                                                 >  2:139954/1‑140 (MQ=255)

   tatTTTTCTAATCTTTTTTTTAGATATTTGAGTATTAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTaa                                                                                                                                <  2:709793/140‑1 (MQ=255)

     ttGTTCTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACa                                                                                                                              <  1:144383/140‑1 (MQ=255)

       gTTCTAATCTTTTTTTTTTATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTTTTTCTTAATTGGACGGTTTTAACatt                                                                                                                            >  2:326425/1‑138 (MQ=255)

       gTTCTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGt                                                                                                                            >  1:652369/1‑140 (MQ=255)

          cTAATCTTTTTTTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCAt                                                                                                                         <  1:263181/140‑1 (MQ=255)

          cTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCAt                                                                                                                         <  1:522363/140‑1 (MQ=255)

           tAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATa                                                                                                                        <  2:667312/140‑1 (MQ=255)

             aTCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACCGTCATCCa                                                                                                                      >  2:305154/1‑140 (MQ=255)

              tCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACaa                                                                                                                     >  2:63985/1‑140 (MQ=255)

                tttttGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAAt                                                                                                                   >  1:164710/1‑140 (MQ=255)

                 ttttGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAAtt                                                                                                                  >  1:43030/1‑140 (MQ=255)

                     gTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGGCATCAATTTATTACTTTCTAAAAAATATTCAGTTACAAATGTTTATGAATTGACCGGTTTTAAAAGGAATCCAAATTTTGc                                                                                                              >  1:238571/1‑140 (MQ=255)

                          ttttttGAGTATGAATATTAAAGATTATTTTACAAGTATTAAACTTGTTAAAGCCATCAATTTATTACTTTTTACATATCATTTTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTTATAAAAATTTTACAAAta                                                                                                         >  2:410304/4‑139 (MQ=255)

                                     tGAATTTTAGAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAAt                                                                                              >  1:532859/1‑140 (MQ=255)

                                          tttAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACtt                                                                                         <  1:454232/140‑1 (MQ=255)

                                            tAATGATTATTTTACTAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGc                                                                                       <  1:293775/140‑1 (MQ=255)

                                            tAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGc                                                                                       <  1:402336/140‑1 (MQ=255)

                                             aaaGATTATTTTACAAGGATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGACTTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTACGCATAACtgtaa                                                                                      >  2:6795/1‑136 (MQ=255)

                                              aaGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCAt                                                                                     >  1:155388/1‑140 (MQ=255)

                                               aGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCAtt                                                                                    >  1:488816/1‑140 (MQ=255)

                                                gATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACTTTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCAttt                                                                                   >  1:440502/1‑140 (MQ=255)

                                                      tttACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTcc                                                                             >  1:591208/1‑140 (MQ=255)

                                                                ttAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTc                                                                   <  1:63985/140‑1 (MQ=255)

                                                                  aaaCTTGTTAACGCCATCAAATTATTACTTTCTACAAAACATTCAATTACAAATGTTTATGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTACGAATTACTTGCATTTTAGCCCTAAACAGTTCCg                                                                 >  1:442292/1‑140 (MQ=255)

                                                                  aaaCTTGTTAACGCAATCAATTTATTACTTGCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCg                                                                 <  2:382445/140‑1 (MQ=255)

                                                                      ttGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCa                                                             >  2:396905/1‑140 (MQ=255)

                                                                           aaCGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCACTTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCgg                                                        >  2:678276/1‑139 (MQ=255)

                                                                           aaCGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGt                                                        >  2:599156/1‑140 (MQ=255)

                                                                              gCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTc                                                     <  1:139954/140‑1 (MQ=255)

                                                                                 aTCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCaa                                                  >  1:565106/1‑140 (MQ=255)

                                                                                 aTCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCaa                                                  >  1:14578/1‑140 (MQ=255)

                                                                                 aTCAATTTATTACTTTATACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCTTAAACAGTTCCGTTCACTCGTTTCTaa                                                  >  2:657459/1‑140 (MQ=255)

                                                                                        tattaCTTTCTACAAAACATTCTATTACAACTGTTTCTGAAATGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACt                                           >  1:497269/1‑140 (MQ=255)

                                                                                             cTTTCTACAAAACATCCTATTACATCTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAAGTAATTTAAGAATGACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAacc                                      <  1:183326/140‑1 (MQ=255)

                                                                                                 ctaacaaaCAAGCTATTACAACTGTTTCGGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAAccacca                                  <  1:91597/135‑1 (MQ=255)

                                                                                                 ccaCAAAACATTCTATCACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAAccacca                                  <  1:554433/138‑1 (MQ=255)

                                                                                                  tACAAAACATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACcaccac                                 >  1:536623/1‑140 (MQ=255)

                                                                                                      aaaCATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAAt                             >  2:386234/1‑140 (MQ=255)

                                                                                                         cATTCTATTACAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATaca                          >  1:154476/1‑140 (MQ=255)

                                                                                                                 tACAGCTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAAGGACTTGCATTTTAGTCCTAACCAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTCcaac                  <  2:183974/140‑1 (MQ=255)

                                                                                                                  aCAACTGTTTCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTCcaaca                 >  1:688851/1‑140 (MQ=255)

                                                                                                                         tttCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTCCAACAAGATAAc          >  1:689525/1‑140 (MQ=255)

                                                                                                                          ttCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACGCCCACAAATACACTTCCAACAAGATAACg         >  1:700087/1‑140 (MQ=255)

                                                                                                                          ttCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTCCAACAAGATAACg         <  2:154708/140‑1 (MQ=255)

                                                                                                                           tCTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCAGTCGTTTCCAAGATTACTGAACAAACCAAAATACACTTTAAAAAAGATacagt        >  1:293366/1‑136 (MQ=255)

                                                                                                                            cTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTCCAACAAGATAACGTa       >  1:676191/1‑140 (MQ=255)

                                                                                                                            cTGAATTGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTCCAACAAGATAACGTa       >  2:314155/1‑140 (MQ=255)

                                                                                                                             tGAATTGGACGGTTTTAACAGTCATACACATTTTGCAAATCAATTTAAGAATTACTTGCATTGTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATAAACTTCCAACAAGATAACGTag      >  2:434272/1‑139 (MQ=255)

                                                                                                                                 ttGGACGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTCCAACAAGATAACGTATcaca  <  2:705327/140‑1 (MQ=255)

TCATATTGTTCTAATCTTTTTGTTCGATATTTGAGTATGAATTTTAAAGATTATTTTACAAGTATTAAACTTGTTAACGCCATCAATTTATTACTTTCTACAAAACATTCTATTACAACTGTTTCTGAATTGGCCGGTTTTAACAGTCATACAAATTTTGCAAATCAATTTAAGAATTACTTGCATTTTAGTCCTAAACAGTTCCGTTCACTCGTTTCCAAGATTACTGAACCACCACAAATACACTTCCAACAAGATAACGTATCACA  >  CP000730/2502008‑2502276

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A