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
A9 F59 I0 R1	41	42.9	928050	95.2%	883503	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,963,768	C→G	100%	V365L (GTA→CTA)	hemG ←	protoporphyrinogen oxidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,963,768	0	C	G	100.0%	166.9 / NA	49	V365L (GTA→CTA)	hemG	protoporphyrinogen oxidase
Reads supporting (aligned to +/- strand): ref base C (0/0); new base G (27/22); total (27/22)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CGGCAAACGATTGACAATTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTATTTTCAATGTCT  >  CP000730/1963637‑1963904

cGGCAAACGATTGACCATTGCTATTTCATGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGGTACGccag                                                                                                                                 >  2:211954/1‑138 (MQ=255)

cGGCAAACGATTGACAATTGTAAATTCAGGATCACCTTTAAGTGTCATCAATTGACTTAAATCTCTACGTACAATCCATACTAATTCATTATCTGTATGATCATCAACCACAGCAACACCTGGCTTACCTCGATACGCACg                                                                                                                                 >  2:196995/1‑141 (MQ=255)

   cAAACGATTGACAATTGTAAATTCAGGGTCACGTTTAAATGTCATCTTTTGTCTGAATTTACATCGTACAATTGATACTAATTCATTATCTGTATGATCATACACCACGGGATCACCTGGTTTACCTAGATCCGccgaaaa                                                                                                                              >  2:151782/1‑135 (MQ=255)

    aaaCGATTGACAATTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGACTc                                                                                                                             <  2:232511/141‑1 (MQ=255)

        gATTGACAATTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCaaaa                                                                                                                         >  1:114626/1‑141 (MQ=255)

             aCAATTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAacctta                                                                                                                    <  2:235830/141‑1 (MQ=255)

              cAATTGTAAATTCAGGATCACCTTTAAATGCCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAaccttac                                                                                                                   <  1:10969/141‑1 (MQ=255)

                   gTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTcc                                                                                                              <  2:111776/141‑1 (MQ=255)

                     aaaTTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTCTCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCgg                                                                                                            <  2:296993/141‑1 (MQ=255)

                     aaaTTCAGGACCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCgg                                                                                                            <  1:56810/141‑1 (MQ=255)

                        ttCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGgtgt                                                                                                         >  1:164489/1‑141 (MQ=255)

                                    tttAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTTAATGGCCa                                                                                             >  2:21635/1‑141 (MQ=255)

                                    tttAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCa                                                                                             >  1:165102/1‑141 (MQ=255)

                                         aTGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATAACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTACCGGTGTAGTAACTGGCCattatt                                                                                        >  2:199909/1‑141 (MQ=255)

                                           gTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTc                                                                                      <  1:198742/141‑1 (MQ=255)

                                           gTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTc                                                                                      <  1:170263/141‑1 (MQ=255)

                                                      aCTTAAATCTCTACGTACACTCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGt                                                                           <  1:103376/141‑1 (MQ=255)

                                                      aCTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGt                                                                           <  1:354575/141‑1 (MQ=255)

                                                      aCTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGGATGATCATCCACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGt                                                                           <  2:171231/141‑1 (MQ=255)

                                                                ctACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTGACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCGTTTTTTCGATGTCCAAGTACATGCGGTa                                                                 <  1:298183/141‑1 (MQ=255)

                                                                 tACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACCTGAggaag                                                                >  2:113855/1‑138 (MQ=255)

                                                                     tACAATCGATACGAATTCATTCTCTGTATGATCATCAACCACAGTAGCACCTGGTGTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTGGAAGATGGACATTTTTTACAGGTCCAAGTACATGCGGTaagggt                                                            >  2:378065/1‑137 (MQ=255)

                                                                      aCAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCt                                                           >  2:79303/1‑141 (MQ=255)

                                                                           cGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACGTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATc                                                      >  1:237490/1‑141 (MQ=255)

                                                                            gATACGAGTTCATTTACCGTATGACCATCAACCCTAGTAGCACCTGGTTCACCTCGATACGCACGAATCAAAACCTTTCCTTCCGGTGTAGTAAATGGCCATTTCTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCa                                                     <  2:351588/141‑1 (MQ=255)

                                                                                   aTTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGtcc                                              >  2:342978/1‑139 (MQ=255)

                                                                                   aTTCATTATCTGTATGATCATCAACCACAGTATAACATGGTTTACCTAGATACGTTCGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTAAATGCGGTAATGTCTGTATCACTCGttt                                              >  1:411005/1‑140 (MQ=255)

                                                                                          aTCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAAt                                       >  1:345949/1‑141 (MQ=255)

                                                                                          aTCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAAt                                       >  2:51643/1‑141 (MQ=255)

                                                                                           tCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAAtt                                      <  1:193565/141‑1 (MQ=255)

                                                                                            cTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCACGTACATGCGGTAAGGCCTGTATCCGTCTCTCTCGCAATTa                                     >  2:399436/1‑141 (MQ=255)

                                                                                               tATGATCATCAACCACAGTATCACCTGGTCTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGa                                  <  2:372518/141‑1 (MQ=255)

                                                                                                   atcatcAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGcc                              >  1:350430/1‑141 (MQ=255)

                                                                                                       tcaACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGAAATTACGAAGCCAGTa                          >  2:418820/1‑141 (MQ=255)

                                                                                                        caACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGGGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCACTTACGAAGCCAGTAc                         >  1:356/1‑141 (MQ=255)

                                                                                                          aCCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGCTGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCTCAATTACGAAGCCAGTACca                       >  1:18073/1‑141 (MQ=255)

                                                                                                             acaGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGACCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACcatca                    >  2:218192/1‑141 (MQ=255)

                                                                                                                 tATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGGGTAGTAAATGGCAATGGTTTCGATGACCAAGTACCTGAGATAATGAATGTATCACTCGATCTCGCAATTACGAAGCCAGTACCATCATggg                >  2:345269/1‑141 (MQ=255)

                                                                                                                  aTCACCTGTTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGt               <  1:459575/141‑1 (MQ=255)

                                                                                                                  aTCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCTTTGTTTAACTACATGAGATAATGACTATATAATTCGCTCTCGCAATTACGAACCCacaactctcctgggt               >  2:278794/1‑127 (MQ=255)

                                                                                                                  aTCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGt               <  1:171107/141‑1 (MQ=255)

                                                                                                                     aCCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTAtt            >  1:16885/1‑141 (MQ=255)

                                                                                                                      ccTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGCAGCCAGTACCATCATGGGTAttt           <  1:364862/141‑1 (MQ=255)

                                                                                                                         tgtgtACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACGATCATGGGGATTTTCa        <  2:433733/137‑1 (MQ=255)

                                                                                                                          gTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTATTTTCaa       <  1:346894/141‑1 (MQ=255)

                                                                                                                              aCCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATTCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTGTTTTCAAtttt   >  2:120814/1‑138 (MQ=255)

                                                                                                                               ccTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCCCTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTAATGTCAATgctt  >  2:226160/1‑138 (MQ=255)

                                                                                                                               ccTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTATTTTCAATGTCt  <  2:104401/141‑1 (MQ=255)

                                                                                                                               ccTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTATTTTCAATGTCt  <  2:93186/141‑1 (MQ=255)

CGGCAAACGATTGACAATTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTATTTTCAATGTCT  >  CP000730/1963637‑1963904

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