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
A7 F67 I1 R1	27	23.6	499472	97.1%	484987	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	195,286	T→A	intergenic (‑97/‑82)	USA300HOU_0183 ← / → USA300HOU_0184	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	195,286	0	T	A	100.0%	79.6 / NA	24	intergenic (‑97/‑82)	USA300HOU_0183/USA300HOU_0184	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (11/13); total (11/13)

CTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑TAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACG  >  CP000730/195159‑195415

cTAACCCTGCTACCACAGATTACTTATCTATAATGATATCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCtt                                                                                                                      <  1:111632/141‑1 (MQ=255)

  aaaCTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTCTATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTaa                                                                                                                    >  1:341695/1‑141 (MQ=255)

  aaaCTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATTTAATTATT‑ATAAAAATTATCTTat                                                                                                                    >  1:293271/1‑140 (MQ=255)

        gCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCt                                                                                                              >  1:424989/1‑141 (MQ=255)

                              tAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACAGGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGCAATCCGATAAGAATTATAg                                                                                        <  1:264420/141‑1 (MQ=255)

                                        ccccTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATAttttt                                                                              <  1:454098/141‑1 (MQ=255)

                                          ccTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTc                                                                            <  1:43686/141‑1 (MQ=255)

                                          ccTATATATATGGTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTCTAGTAATATTTTTTc                                                                            <  1:368946/141‑1 (MQ=255)

                                           cTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCa                                                                           >  1:410675/1‑141 (MQ=255)

                                                tatatGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCAt                                                                      <  1:140918/141‑1 (MQ=255)

                                                            taCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATaggagg                                                          >  1:172805/1‑141 (MQ=255)

                                                             aCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGt                                                         >  1:497133/1‑141 (MQ=255)

                                                                tataCCCTAACATTATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCtt                                                      <  1:232643/141‑1 (MQ=255)

                                                                tataCCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCtt                                                      <  1:370337/141‑1 (MQ=255)

                                                                tataCCCTAACATGATTTTTATACCCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATACTAATGAGTTTTCAACCATTGTTATAGGAGGTCtt                                                      <  1:493427/141‑1 (MQ=255)

                                                                        aaCATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGa                                              <  1:376884/141‑1 (MQ=255)

                                                                          cATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACa                                            >  1:173985/1‑141 (MQ=255)

                                                                             gATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACatta                                         >  1:219290/1‑141 (MQ=255)

                                                                                  ttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTAttttt                                    >  1:106502/1‑141 (MQ=255)

                                                                                    ataCTCTTTGAAAATAGATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTttat                                  <  1:4483/141‑1 (MQ=255)

                                                                                          tttGAAAATATATTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAg                            <  1:38429/141‑1 (MQ=255)

                                                                                                   atatTTTACAGAATTTTATCTAAATATT‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGACGCTAGCAAtg                   >  1:166156/1‑140 (MQ=255)

                                                                                                      ttttACAGAATTTTATCTAAATATC‑AAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTg                <  1:337344/141‑1 (MQ=255)

                                                                                                                     tCTAAATATTAAAAAAAAATATCTTAATATCCTTATAATCCGATAAGAATGATAGTACTATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTTGAAGCTAAAAATCTTAATTTTGCATCaaag  >  1:341649/1‑139 (MQ=255)

CTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATT‑TAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACG  >  CP000730/195159‑195415

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A