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
A5 F178 I0 R1	41	49.4	1100758	95.6%	1052324	140.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,963,768	C→G	100%	V365L (GTA→CTA)	hemY ←	Protoporphyrinogen oxidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,963,768	0	C	G	96.5%	173.0 / ‑0.9	58	V365L (GTA→CTA)	hemY	Protoporphyrinogen oxidase
Reads supporting (aligned to +/- strand): ref base C (1/1); new base G (33/22); total (34/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.61e-01
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.

CTTTTCGGCAAACGATTGACAATTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTATTTTCAATG  >  USA300TCH1516_ALE/1963632‑1963901

cTTTTCGGCAAACGATTGACAATTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATa                                                                                                                                    >  1:460505/1‑140 (MQ=255)

  tttCGGCAAACGATTGACAATTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACg                                                                                                                                  >  2:394633/1‑140 (MQ=255)

           actaTTGACAATTGTAACTTCAGGATCACCTTTCAAAGTCATCATTTCACTTAAACCTCTACGCACAATCGATACTAATTCAATATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCa                                                                                                                         <  2:190685/137‑1 (MQ=255)

           aCGATTGACAATTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCa                                                                                                                         <  2:489347/140‑1 (MQ=255)

                tGACAATTGTAAATTAAGGATCACCTTTACCTGTCATCATTTGACTTTAATCTCTAAGTGCACTCGATACTAATTCATTATATGTATGATCATCAACCCCAGTATCACCTCGTTTACCTAGATACGCACGGATCATAacc                                                                                                                    >  2:141462/1‑140 (MQ=255)

                  aCAATTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAacctt                                                                                                                  >  2:488146/1‑140 (MQ=255)

                      ttGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACTTTCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAaccttacct                                                                                                              <  1:538255/140‑1 (MQ=255)

                      ttGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTTATTCTTTATATGTATGATCATCAACCACAGTATAACCTGGTTTACCTAGATACGCACGAATCAAAaccttacct                                                                                                              <  1:478337/140‑1 (MQ=255)

                      ttGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAaccttacct                                                                                                              <  2:407615/140‑1 (MQ=255)

                       tGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAaccttacctt                                                                                                             >  1:358102/1‑140 (MQ=255)

                           aaTTCAGGATCACGTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTCGATACCCACGAATCAAAACCTTACCTTCCgg                                                                                                         >  2:524792/1‑140 (MQ=255)

                                  gATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTgtagta                                                                                                  >  2:522313/1‑140 (MQ=255)

                                    tCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTaaa                                                                                                >  2:522208/1‑140 (MQ=255)

                                          ttAAATGTCATCATTTGACTTAAATCTCTACCTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCa                                                                                          <  2:400263/140‑1 (MQ=255)

                                                 tcatcaTTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATTTTCTACCACAGTATCTCCTGGTTTTCTTAGATTCGAGCTATTCATAATCTTTCCTTTCGGTGTAGTAATTGGCATTTTTTTc                                                                                   >  1:125046/1‑140 (MQ=255)

                                                     catTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATg                                                                               >  1:304531/1‑140 (MQ=255)

                                                     catTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATg                                                                               <  1:522313/140‑1 (MQ=255)

                                                     catTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGGATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATg                                                                               <  2:132917/140‑1 (MQ=255)

                                                             ttAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTa                                                                       <  1:504635/140‑1 (MQ=255)

                                                                   ttctACGTACAATTGTTTCTATTTCATGTTTTGTATTATCATCAACCACATTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCg                                                                 <  2:312982/139‑1 (MQ=255)

                                                                    tctACGTACAATCGATACTAATTCATTATCTGTATGATCATCTACCACATTATGACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTGCAAGTACATGCgg                                                                >  1:290993/1‑140 (MQ=255)

                                                                    tcgaCGTACAATCGATACGAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGTTGTTCTAGAACATCCgg                                                                >  2:531725/4‑140 (MQ=255)

                                                                           aCAATCGCTACTAACTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAGACCTTACCTTCTGGCGTAGTAAATGGCCATGTTTTCCATGTCCAAGTGCCTGCggccaggtc                                                         >  2:398387/1‑133 (MQ=255)

                                                                           aCAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCACAACCTTACCTTCCGCTGTAGTAAATGGCCATTTTTTTGATGTCCCAGTACGTGCGGTACTGta                                                         >  2:398386/1‑139 (MQ=255)

                                                                            cAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGAACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTCATGTCt                                                        >  1:139940/1‑140 (MQ=255)

                                                                              aTCGATACTAATTCATTATCTGTATGATCATCAACCACTGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGt                                                      <  1:87414/140‑1 (MQ=255)

                                                                                cGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGGGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAAGATCTGTAt                                                    >  2:515969/1‑140 (MQ=255)

                                                                                 gATACTCATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATc                                                   <  2:435429/140‑1 (MQ=255)

                                                                                 gATACTATTTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATc                                                   <  1:256544/140‑1 (MQ=255)

                                                                                         ttCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTTGATTTTCAATTCCATGCGGTAATGTCTGTATCACTCGTtc                                           >  2:69176/1‑140 (MQ=255)

                                                                                           cATTATCTGTATGATCATCAACCACAGTCTCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCAGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTtctc                                         >  1:355326/1‑140 (MQ=255)

                                                                                           cATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTtctc                                         >  1:418499/1‑140 (MQ=255)

                                                                                            aTTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTAAATGCGGTAATGTATGTATCACTAGTTCTCg                                        <  2:186624/140‑1 (MQ=255)

                                                                                               aTCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCaa                                     >  1:248487/1‑140 (MQ=255)

                                                                                                tCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAAt                                    <  1:228254/140‑1 (MQ=255)

                                                                                                 cTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATAAGCAAGAATAAAAATCTTACATTCAGGTGTAGTAAATGGCAATTTTTTCGATGTCAAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAAtt                                   >  1:18855/1‑140 (MQ=255)

                                                                                                   gTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTAc                                 <  2:399423/140‑1 (MQ=255)

                                                                                                      tGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATTTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGaa                              >  1:352661/1‑140 (MQ=255)

                                                                                                          catcaACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCTTTTTTTCGATGTCAAACTACACGCGTTAAAGTCTGTATCAACCGTTATCGCAATTAAGAAACCa                          >  1:101954/1‑140 (MQ=255)

                                                                                                          catcaACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCTTTTTTTTTTTCCATGCGGACATGTCTGTATCACTCGTTCTCGCCGTTTCGAACCCa                          >  2:146219/1‑140 (MQ=255)

                                                                                                              aaCCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTAc                      >  2:57773/1‑140 (MQ=255)

                                                                                                                 cacaGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTAccgt                   >  2:506970/1‑138 (MQ=255)

                                                                                                                 cacaGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTAAGAAGCCAGTACcat                   >  1:184993/1‑140 (MQ=255)

                                                                                                                 cacaGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGCGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACcat                   >  2:207033/1‑140 (MQ=255)

                                                                                                                 cacaGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCAACGAAGAAAATAGCCATATTATCGATGTCCAAGTACATGCGGTAATGACTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACcat                   >  1:165448/1‑140 (MQ=255)

                                                                                                                 cacaGTATCACCTGGTTTACCTAGATACGCACGAATAAAGACGTAATCGTCCGGTGTAGTAAATGGCCATTTTTTCGTTGTCCAAGTACATGCGGTAATGTCTGTATCACTAGTTCTCGCAATTACGAAAGCAGTACcaa                   >  2:413586/1‑139 (MQ=255)

                                                                                                                 cacaGTATAACTACGGTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAGATGGCCATTTTTTCGATGTCCAACTACATGCGGTAATGTATGTATCACTCGTTCTGCCACTTACGAAGCCAGTACcat                   >  2:172833/1‑140 (MQ=255)

                                                                                                                 cacaGTAACACCTGGTTGACCTAGATACTGGCGAGTGAAAACCTTAGCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTAGTTCTCGCCATTACGAAGCCAGTACcat                   >  2:543763/1‑140 (MQ=255)

                                                                                                                    aGTATCACCTGGTTTACCTAGATACGCACGAATCAACACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACcatcat                >  1:20209/1‑140 (MQ=255)

                                                                                                                     ttATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTATCTTCCTGTGTAGTAAATGGCCAGTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATg               <  1:185646/139‑1 (MQ=255)

                                                                                                                       aTCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATggg             <  1:443890/140‑1 (MQ=255)

                                                                                                                        tCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGt            <  2:117355/140‑1 (MQ=255)

                                                                                                                          aCCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTAt          <  1:216747/140‑1 (MQ=255)

                                                                                                                           ccTCGTTTACCTAGATACCCACGACTCAAAACCTTACCTTCTGGTGTAGTAATTGGTCATTTTTTCGATGTCCAAGTACATGTTGCATTGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTAtt         <  1:457047/140‑1 (MQ=255)

                                                                                                                             tGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTTGTTTTTTAATTACATGCGGGAATGTCTGTATAACTCGTTCTCTCGATTACGAAGCCACTACCAGCATGGGTActtc       >  2:236091/1‑139 (MQ=255)

                                                                                                                               gTTTACCTAGATACGCACGAATCAAAACCTTATCTTCCGTTGTAGTAAATTGCCATTTTTTCGATGTCCAATTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTATTTTCa     <  1:27430/140‑1 (MQ=255)

                                                                                                                               gTTGACCTTTATACTCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTATTTTCa     <  2:487785/140‑1 (MQ=255)

                                                                                                                                  tACCTAGATACGCACTAATCAAAACCGTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTATTTTCAATg  <  2:447902/140‑1 (MQ=255)

CTTTTCGGCAAACGATTGACAATTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTATTTTCAATG  >  USA300TCH1516_ALE/1963632‑1963901

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