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	1,419,527	G→T	100%	P7T (CCT→ACT)	USA300HOU_1317 ←	hypothetical membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,419,527	0	G	T	100.0%	156.9 / NA	55	P7T (CCT→ACT)	USA300HOU_1317	hypothetical membrane protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (23/32); total (23/32)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTTGGAATAAAAAATGCAAGCACACCTAATATAACAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATTCTATCTACTAATAGAAAAATCATT  >  CP000730/1419394‑1419663

tttGGAATAAAAAATGCAAGCACACCTAATATAACAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAGTGTTGTGATCCCTAAATAATTAGTCATATc                                                                                                                                    >  1:553196/1‑140 (MQ=255)

    gAATAAAAAATGCAAGCACACCTAATATAACAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATGTTGTTAATAAAATCATTATCAAGGTTGTTATCCATAAATAATTAGTCATATCGaat                                                                                                                                <  1:645867/140‑1 (MQ=255)

    gAATAAAAAATGCAAGCACACCTAATATAACAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGaat                                                                                                                                >  2:128526/1‑140 (MQ=255)

      aTAAAAAATGCAAGCACACCTAATATAACAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTGGTCATATCGaataa                                                                                                                              <  1:400357/140‑1 (MQ=255)

                  aGCACACCTAATATAACAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATattcat                                                                                                                  >  1:208701/1‑140 (MQ=255)

                  aGCACACCTAATATAACAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATattcat                                                                                                                  >  2:675237/1‑140 (MQ=255)

                        ccTAATATAACAAATGTAATTACTGCAGATAAAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCt                                                                                                            <  1:258850/140‑1 (MQ=255)

                            atatAACAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTa                                                                                                        >  1:506154/1‑140 (MQ=255)

                               taACAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTAttt                                                                                                     <  1:219093/140‑1 (MQ=255)

                                 aCAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATACATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCa                                                                                                   <  2:374392/140‑1 (MQ=255)

                                 aCAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCa                                                                                                   <  1:46868/140‑1 (MQ=255)

                                 aCAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCa                                                                                                   <  1:249410/140‑1 (MQ=255)

                                  cAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCAt                                                                                                  >  2:44911/1‑140 (MQ=255)

                                   aaaggcaaTTACTGTAGACTAAAACCATTTATTTAAAACTAAGCACCAGAATATTGTTAATAAAATCATTATTAATTTTGTTATCCATAAATAATTAGTCGTATCGATTGCTGTCATATTCATTCTCCTTTTATTTCAtt                                                                                                 <  2:133403/134‑1 (MQ=255)

                                   aaaTGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCAtt                                                                                                 <  2:615115/140‑1 (MQ=255)

                                    aaTGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTa                                                                                                <  2:215354/140‑1 (MQ=255)

                                    aaTGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTa                                                                                                <  1:267296/140‑1 (MQ=255)

                                     aTGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTAc                                                                                               <  2:681772/140‑1 (MQ=255)

                                       gTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATTGAATAATGTGATATTCATTCTCCTTTTATTTCATTCCtt                                                                                             >  1:57414/1‑140 (MQ=255)

                                         aaTTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTc                                                                                           >  1:564874/1‑140 (MQ=255)

                                         aaTTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTATCTTATTTTTTCATTTGTTTc                                                                                           >  2:603543/1‑140 (MQ=255)

                                           ttATTGCAGTTACATATCATTTATTTAAAACTGAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCt                                                                                         <  1:493252/140‑1 (MQ=255)

                                               ttcaactgcacaCCTTTTATTGAAAACGAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTGATTTCATTACTTTCCTTGta                                                                                     <  2:566137/129‑1 (MQ=255)

                                               tGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGta                                                                                     >  2:261240/1‑140 (MQ=255)

                                               tGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGta                                                                                     >  2:375587/1‑140 (MQ=255)

                                                gCATATACAAACCAATTATTGAAAACTAAGCAACATAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGtat                                                                                    <  1:373261/140‑1 (MQ=255)

                                                   gATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACa                                                                                 <  2:670488/140‑1 (MQ=255)

                                                       cAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACAtttt                                                                             >  2:601994/1‑140 (MQ=255)

                                                        aaaCCATTTATTTAAAACTAAGCCATCGATTATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTAATTACTTTCCTTGTATACATTtta                                                                            >  2:334004/1‑140 (MQ=255)

                                                         aaCCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTttat                                                                           <  2:375616/140‑1 (MQ=255)

                                                                tatttaAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATTATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAAt                                                                    <  1:447273/140‑1 (MQ=255)

                                                                      aaaCTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTaa                                                              >  2:123859/1‑140 (MQ=255)

                                                                      aaaCTAAGCAACACAATATTTTTAATAAAATCTCTATCATTGCAATAAACCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTaa                                                              <  1:313111/140‑1 (MQ=255)

                                                                        aCTAATCAACAGAATATTGTTAATAAAATCATTATTAATTTTCTGATCCATAAATAATTAGTTATATCGAATAATTTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTaaaa                                                            <  2:271110/140‑1 (MQ=255)

                                                                        aCTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTaaaa                                                            >  1:659972/1‑140 (MQ=255)

                                                                            aGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACtt                                                        <  1:269430/140‑1 (MQ=255)

                                                                              cAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTaa                                                      <  2:49349/140‑1 (MQ=255)

                                                                               aaCAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAATTTTTTAAAAACTTaaa                                                     >  1:289463/1‑140 (MQ=255)

                                                                               aaCAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACAGTTTATTATAAATTTTTACAAACGTaaa                                                     >  2:580702/1‑140 (MQ=255)

                                                                                     atatTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTACAAACTTAAACAATAg                                               >  2:588139/1‑140 (MQ=255)

                                                                                      tatTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGc                                              <  2:212756/140‑1 (MQ=255)

                                                                                             aataaAATCATTATTAATGTTGTGATCCACAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGcagtcagt                                       >  1:719174/1‑140 (MQ=255)

                                                                                                  aaTCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCaa                                  <  1:675237/140‑1 (MQ=255)

                                                                                                  aaTCATTATTAATGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCaa                                  <  1:410153/140‑1 (MQ=255)

                                                                                                          ttaATGTTGTGATCCATAAATAATTAGTCATATCGAATAAAGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATATTATTATAAAATTATAAAAACTTAAACAATAGCAGACAGCTTCAAACAataat                          >  1:226544/1‑138 (MQ=255)

                                                                                                           taATGTTGTGATCCATAAATAATTCGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTGATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAACACTTCAACAGTAGCAGTCCGTTTctacgaatcttc                         >  2:67586/1‑129 (MQ=255)

                                                                                                            aaTGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATtct                        >  2:632612/1‑140 (MQ=255)

                                                                                                            aaTGTTGTGATCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATtct                        <  1:357024/140‑1 (MQ=255)

                                                                                                                   tcaTCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATTCTATctact                 <  2:272013/138‑1 (MQ=255)

                                                                                                                     aTCCATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATTCTATCTACTaa               <  1:375587/140‑1 (MQ=255)

                                                                                                                      tCCATAAATAATTAGTCATATCGAATAATGTTATATTCATTCTCCTTTTATTTCATTAATTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAATAATAGCAGTCAGTTTCAAGCAATATtctaaaaaaaaaa              <  2:533217/140‑10 (MQ=255)

                                                                                                                        cATAAATAATTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATTCTATCTACTAATAg            <  2:208701/140‑1 (MQ=255)

                                                                                                                            aataatTAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATTCTATCTACTAATAGacaa        >  2:510419/1‑140 (MQ=255)

                                                                                                                                 ttAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATTCTATCTACTAATAGAAAAATCAt   <  1:90433/140‑1 (MQ=255)

                                                                                                                                  tAGTCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATTCTATCTACTAATAGAAAAATCAtt  <  2:185463/140‑1 (MQ=255)

TTTGGAATAAAAAATGCAAGCACACCTAATATAACAAATGTAATTACTGCAGATACAAACCATTTATTTAAAACTAAGCAACAGAATATTGTTAATAAAATCATTATTAATGTTGTGATCCATAAATAATTAGGCATATCGAATAATGTCATATTCATTCTCCTTTTATTTCATTACTTTCCTTGTATACATTTTATTATAAATTTTTAAAAACTTAAACAATAGCAGTCAGTTTCAAGCAATATTCTATCTACTAATAGAAAAATCATT  >  CP000730/1419394‑1419663

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