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
A2 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,906,823	A→G	38.0%	N881N (AAT→AAC)	recC ←	exonuclease V (RecBCD complex), gamma chain

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,906,823	0	A	G	38.0%	30.9 / 39.1	63	N881N (AAT→AAC)	recC	exonuclease V (RecBCD complex), gamma chain
Reads supporting (aligned to +/- strand): ref base A (15/24); new base G (15/9); total (30/33)
Fisher's exact test for biased strand distribution p-value = 7.50e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.64e-01

CGGAAGCGGCGGAACAAGCGTTCGGCATCATCCTGCTCAACCAGTGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATAAATGGCTCGGTGTCGGGGATTTCGCTG  >  minE/1906761‑1906883

cGGAAGCGGCGGAACAAGCGTTCGGCATCATCCTGCTCAACCAGTGCATTCAATAACTGCtgattgat                                                         >  1:1418071/1‑68 (MQ=255)

  gAATCGGCGGAACAAGCGTTCGGCATCATCCTGCTCAACCAGTACATTTAATAACTGCTGGttgattt                                                       >  1:943339/1‑68 (MQ=255)

  gAATCGGCGGAACAAGCGTTCGGCATCATCCTGCTCAACCAGTACATTTAATAACTGCTGGttgattt                                                       >  1:2097579/1‑68 (MQ=255)

  gAATCGGCGGAACAAGCGTTCGGCATCATCCTGCTCAACCAGTACATTTAATAACTGCTGGttgattt                                                       >  1:1963765/1‑68 (MQ=255)

  gAATCGGCGGAACAAGCGTTCGGCATCATCCTGCTCAACCAGTACATTTAATAACTGCTGGttgattt                                                       >  1:2490447/1‑68 (MQ=255)

  gAATCGGCGGAACAAGCGTTCGGCATCATCCTGCTCAACCAGTACATTTAATAACTGCTGGttgattt                                                       >  1:1691023/1‑68 (MQ=255)

  gAATCGGCGGAACAAGCGTTCGGCATCATCCTGCTCAACCAGTACATTTAATAACTGCTGGttgattt                                                       >  1:2528150/1‑68 (MQ=255)

  gAATCGGCGGAACAAGCGTTCGGCATCATCCTGCTCAACCAGTACATTTAATAACTGCTGGttgattt                                                       >  1:1566964/1‑68 (MQ=255)

  gAATCGGCGGAACAAGCGTTCGGCATCATCCTGCTCAACCAGTACATTTAATAACTGCTGGttgattt                                                       >  1:1511111/1‑68 (MQ=255)

  gAATCGGCGGAACAAGCGTTCGGCATCATCCTGCTCAACCAGTACATTTAATAACTGCTGGttgattt                                                       >  1:3205987/1‑68 (MQ=255)

  gAATCGGCGGAACAAGCGTTCGGCATCATCCTGCTCAACCAGTACATTTAATAACTGCTGGttgattt                                                       >  1:526575/1‑68 (MQ=255)

  gAATCGGCGGAACAAGCGTTCGGCATCATCCTGCTCAACCAGTACATTTAATAACTGCTGGttgattt                                                       >  1:680342/1‑68 (MQ=255)

  gAATCGGCGGAACAAGCGTTCGGCATCATCCTGCTCAACCAGTACATTTAATAACTGCTGGttgattt                                                       >  1:1384200/1‑68 (MQ=255)

  gAATCGGCGGAACAAGCGTTCGGCATCATCCTGCTCAACCAGTACATTTAATAACTGCTGGttgattt                                                       >  1:812086/1‑68 (MQ=255)

  gAATCGGCGGAACAAGCGTTCGGCATCATCCTGCTCAACCAGTACATTTAATAACTGCTGGttgattt                                                       >  1:89792/1‑68 (MQ=255)

  gAATCGGCGGAACAAGCGTTCGGCATCATCCTGCTCAACCAGTACATTTAATAACTGCTGGttgattt                                                       >  1:943275/1‑68 (MQ=255)

                           tcatcCTGCTCAACCAGTGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATa                             >  1:1557466/1‑69 (MQ=255)

                            catcCTGCTCAACCAGTGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATaa                            >  1:2368466/1‑69 (MQ=255)

                             atcCTGCTCAACCAGTGCATTCAATAAGTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATaaa                           >  1:3311554/1‑69 (MQ=255)

                             atcCTGCTCAACCAGTGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAg                                          <  1:2895723/54‑1 (MQ=255)

                             atcCTGCTCAACCAGTGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAg                                          <  1:2593536/54‑1 (MQ=255)

                             atcCTGCTCAACCAGTGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAg                                          <  1:2525392/54‑1 (MQ=255)

                             atcCTGCTCAACCAGTGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAg                                          <  1:2377788/54‑1 (MQ=255)

                             atcCTGCTCAACCAGTGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAg                                          <  1:2557052/54‑1 (MQ=255)

                             atcCTGCTCAACCAGTGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAg                                          <  1:2275628/54‑1 (MQ=255)

                             atcCTGCTCAACCAGTGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAg                                          <  1:147201/54‑1 (MQ=255)

                             atcCTGCTCAACCAGTGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATaaa                           >  1:2325553/1‑69 (MQ=255)

                             atcCTGCTCAACCAGTGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATaaa                           >  1:1851003/1‑69 (MQ=255)

                             atcCTGCTCAACCAGTGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATaaa                           >  1:1460985/1‑69 (MQ=255)

                             atcCTGCTCAACCAGTGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATaaa                           >  1:516243/1‑69 (MQ=255)

                             atcCTGCTCAACCAGTGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATaaa                           >  1:460544/1‑69 (MQ=255)

                             atcCTGCTCAACCAGTGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATaaa                           >  1:2536018/1‑69 (MQ=255)

                             atcCTGCTCAACCAGTGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATaaa                           >  1:415870/1‑69 (MQ=255)

                             atcCTGCTCAACCAGTGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATaaa                           >  1:36514/1‑69 (MQ=255)

                             atcCTGCTCAACCAGTGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATaaa                           >  1:1254282/1‑69 (MQ=255)

                             atcCTGCTCAACCAGTGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAGTCCATCCAGAATaaa                           >  1:342458/1‑69 (MQ=255)

                                 tGCTCAACCAGTGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAg                                          <  1:865275/50‑1 (MQ=255)

                                          aGTGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAg                                          <  1:3278616/41‑1 (MQ=255)

                                          aGTACATTTAATAACTGCTGGTTGATTTGATAACGACTAAGCCCTTCAAGAATAAAAGGTTCGGTGTCg              <  1:673624/69‑1 (MQ=255)

                                          aGTACATTTAATAACTGCTGGTTGATTTGATAACGACTAAGCCCTTCAAGAATAAAAGGTTCGGTGTCg              <  1:599713/69‑1 (MQ=255)

                                          aGTACATTTAATAACTGCTGGTTGATTTGATAACGACTAAGCCCTTCAAGAATAAAAGGTTCGGTGTCg              <  1:738841/69‑1 (MQ=255)

                                          aGTACATTTAATAACTGCTGGTTGATTTGATAACGACTAAGCCCTTCAAGAATAAAAGGTTCGGTGTCg              <  1:2891039/69‑1 (MQ=255)

                                          aGTACATTTAATAACTGCTGGTTGATTTGATAACGACTAAGCCCTTCAAGAATAAAAGGTTCGGTGTCg              <  1:881352/69‑1 (MQ=255)

                                          aGTACATTTAATAACTGCTGGTTGATTTGATAACGACTAAGCCCTTCAAGAATAAAAGGTTCGGTGTCg              <  1:1037745/69‑1 (MQ=255)

                                          aGTACATTTAATAACTGCTGGTTGATTTGATAACGACTAAGCCCTTCAAGAATAAAAGGTTCGGTGTCg              <  1:1675536/69‑1 (MQ=255)

                                          aGTACATTTAATAACTGCTGGTTGATTTGATAACGACTAAGCCCTTCAAGAATAAAAGGTTCGGTGTCg              <  1:1815125/69‑1 (MQ=255)

                                          aGTACATTTAATAACTGCTGGTTGATTTGATAACGACTAAGCCCTTCAAGAATAAAAGGTTCGGTGTCg              <  1:1846049/69‑1 (MQ=255)

                                            tGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATAAATGGCTCGGTGTCggg            <  1:3297055/69‑1 (MQ=255)

                                            tGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATAAATGGCTCGGTGTCggg            <  1:3363910/69‑1 (MQ=255)

                                            tGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATAAATGGCTCGGTGTCggg            <  1:1411334/69‑1 (MQ=255)

                                            tGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAGTCCTTACAGAATAAATGGCTCGGTGTCggg            <  1:1069896/69‑1 (MQ=255)

                                                  cAATAACTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATAAATGGCTCGGTGTCGGGGATTTc      >  1:1371194/1‑69 (MQ=255)

                                                  cAATAACTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATAAATGGCTCGGTGTCGGGGATTTc      >  1:1557385/1‑69 (MQ=255)

                                                     tAACTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATAAATGGCTCGGTGTCGGGGATTTCGCt   <  1:3404391/69‑1 (MQ=255)

                                                     tAACTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATAAATGGCTCGGTGTCGGGGATTTCGCt   <  1:664917/69‑1 (MQ=255)

                                                     tAACTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATAAATGGCTCGGTGTCGGGGATTTCGCt   <  1:580349/69‑1 (MQ=255)

                                                     tAACTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATAAATGGCTCGGTGTCGGGGATTTCGCt   <  1:1526572/69‑1 (MQ=255)

                                                      aaCTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATAAATGGCTCGGTGTCGGGGATTTCGCt   <  1:2828044/68‑1 (MQ=255)

                                                       aCTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATAAATGGCTCGGTGTCGGGGATTTCGCTg  <  1:1501445/68‑1 (MQ=255)

                                                       aCTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATAAATGGCTCGGTGTCGGGGATTTCGCTg  <  1:831050/68‑1 (MQ=255)

                                                       aCTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATAAATGGCTCGGTGTCGGGGATTTCGCTg  <  1:2856204/68‑1 (MQ=255)

                                                       aCTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATAAATGGCTCGGTGTCGGGGATTTCGCTg  <  1:1856826/68‑1 (MQ=255)

                                                       aCTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATAAATGGCTCGGTGTCGGGGATTTCGCTg  <  1:1069402/68‑1 (MQ=255)

                                                          gctgATTGATTTGATAACGGCTAAGTCCTTCCAGAATAAATGGCTCGGTGTCGGGGATTTCGCTg  <  1:290051/65‑1 (MQ=255)

CGGAAGCGGCGGAACAAGCGTTCGGCATCATCCTGCTCAACCAGTGCATTCAATAACTGCTGATTGATTTGATAACGGCTAAGTCCTTCCAGAATAAATGGCTCGGTGTCGGGGATTTCGCTG  >  minE/1906761‑1906883

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A