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	441,078	A→G	62.6%	G163G (GGT→GGC)	potE ←	putrescine/proton symporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	441,078	0	A	G	62.6%	33.8 / 31.5	56	G163G (GGT→GGC)	potE	putrescine/proton symporter
Reads supporting (aligned to +/- strand): ref base A (14/7); new base G (27/8); total (41/15)
Fisher's exact test for biased strand distribution p-value = 5.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATGCGGATTCCAGGAATCAACGTACAGCGTCGGGCTAAACCAGAACCAGCCAATAATGCACAGACCGACGACCGGAATAATGACCCCCCACACGGTAATGCTACTGATTTGCCCGGTAATGCG  >  minE/441015‑441137

atgCGGATTCCAGGAATCAACGTACAGCGTCGGGCTAAACCAGAACCAGCCAATAATGCACAGACcgac                                                        >  1:7307/1‑69 (MQ=255)

      aTTCCAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGcct                                                          >  1:2498096/1‑60 (MQ=255)

      aTTCCAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGcct                                                          >  1:2478896/1‑60 (MQ=255)

      aTTCCAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGcct                                                          >  1:2754060/1‑60 (MQ=255)

      aTTCCAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGcct                                                          >  1:1123511/1‑60 (MQ=255)

      aTTCCAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGcct                                                          >  1:1192740/1‑60 (MQ=255)

      aTTCCAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGcct                                                          >  1:535071/1‑60 (MQ=255)

      aTTCCAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGcct                                                          >  1:3166485/1‑60 (MQ=255)

      aTTCCAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGcct                                                          >  1:1252801/1‑60 (MQ=255)

      aTTCCAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGcct                                                          >  1:3393584/1‑60 (MQ=255)

      aTTCCAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGcct                                                          >  1:3237410/1‑60 (MQ=255)

      aTTCCAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGcct                                                          >  1:1846200/1‑60 (MQ=255)

      aTTCCAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGcct                                                          >  1:3340269/1‑60 (MQ=255)

      aTTCCAGGAATCAACGTAAAGTGTAGGGCTAAACCAGAACCAGCCGATAATGCACAGGcct                                                          >  1:2800480/1‑60 (MQ=255)

         ccAGGAATCAACGTACAGCGTCGGGCTAAACCAGAACCAGCCAATAATGCACAGACCGACGACCGGaat                                               >  1:3101177/1‑69 (MQ=255)

         ccAGGAATCAACGTACAGCGTCGGGCTAAACCAGAACCAGCCAATAATGCACAGACCGACGACCGGaat                                               <  1:1969284/69‑1 (MQ=255)

         ccAGGAATCAACGTACAGCGTCGGGCTAAACCAGAACCAGCCAATAATGCACAGACCGACGACCGGaat                                               <  1:1453806/69‑1 (MQ=255)

         ccAGGAATCAACGTACAGCGTCGGGCTAAACCAGAACCAGCCAATAATGCACAGACCGACGACCGGaat                                               <  1:1237639/69‑1 (MQ=255)

          cAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGCCTACCACCGGaata                                              >  1:1499974/1‑69 (MQ=255)

          cAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGCCTACCACCGGaata                                              >  1:1454413/1‑69 (MQ=255)

          cAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGCCTACCACCGGaata                                              >  1:2779645/1‑69 (MQ=255)

          cAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGCCTACCACCGGaata                                              >  1:1940286/1‑69 (MQ=255)

          cAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGCCTACCACCGGaata                                              >  1:196640/1‑69 (MQ=255)

          cAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGCCTACCACCGGaata                                              >  1:1380532/1‑69 (MQ=255)

          cAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGCCTACCACCGGaata                                              >  1:3209070/1‑69 (MQ=255)

          cAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGCCTACCACCGGaata                                              >  1:2264645/1‑69 (MQ=255)

          cAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGCCTACCACCGGaata                                              >  1:1097818/1‑69 (MQ=255)

          cAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGCCTACCACCGGaata                                              >  1:1069910/1‑69 (MQ=255)

          cAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGCCTACCACCGGaata                                              >  1:3001096/1‑69 (MQ=255)

          cAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGCCTACCACCGGaat                                               >  1:2189682/1‑68 (MQ=255)

          cAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGCCTACCACCGGaat                                               >  1:942764/1‑68 (MQ=255)

          cAGGAATCAACGTAAAGTGTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGCCTACCACCGGaa                                                >  1:574001/1‑67 (MQ=255)

                  aaCGTACAGCGTCGGGCTAAACCAGAACCAGCCAATAATGCACAGACCGACGACCGGAATAATGAccc                                       >  1:3325297/1‑68 (MQ=255)

                    cGTACAGCGTCGGGCTAAACCAGAACCAGCCAATAATGCACAGATCGACGACCGGAATAATGAccccc                                     <  1:1342493/68‑1 (MQ=255)

                           tgTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGCCTACCACCGGAATAATGACCCCCCACACGGt                             <  1:3157311/68‑1 (MQ=255)

                           tgTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGCCTACCACCGGAATAATGACCCCCCACACGGt                             <  1:2222550/68‑1 (MQ=255)

                           tgTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGCCTACCACCGGAATAATGACCCCCCACACGGt                             <  1:2626151/68‑1 (MQ=255)

                           tgTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGCCTACCACCGGAATAATGACCCCCCACACGGt                             <  1:2153518/68‑1 (MQ=255)

                           tgTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGCCTACCACCGGAATAATGACCCCCCACACGGt                             <  1:2042939/68‑1 (MQ=255)

                           tgTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGCCTACCACCGGAATAATGACCCCCCACACGGt                             <  1:1878285/68‑1 (MQ=255)

                           tgTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGCCTACCACCGGAATAATGACCCCCCACACGGt                             <  1:1771044/68‑1 (MQ=255)

                           tgTCGGGCTAAACCAGAACCAGCCGATAATGCACAGGCCTACCACCGGAATAATGACCCCCCACACGGt                             <  1:1044461/68‑1 (MQ=255)

                                    aaaCCAGAACCAGCCAATAATGCACAGACCGACGACCGGAATAATGACCCCCCACACGGTAATGCTACt                    <  1:2475284/69‑1 (MQ=255)

                                    aaaCCAGAACCAGCCAATAATGCACAGACCGACGACCGGAATAATGACCCCCCACACGGTAATGCTACt                    <  1:1563941/69‑1 (MQ=255)

                                    aaaCCAGAACCAGCCAATAATGCACAGACCGACGACCGGAATAATGACCCCCCACACGGTAATGCTACt                    <  1:1295316/69‑1 (MQ=255)

                                                       atGCACAGACCGACGACCGGAATAATGACCCCCCACACGGTAATGCTACTGATTTGc             >  1:289816/1‑57 (MQ=255)

                                                       atGCACAGACCGACGACCGGAATAATGACCCCCCACACGGTAATGCTACTGATTTGCCCGGTAATgcg  >  1:867342/1‑68 (MQ=255)

                                                       atGCACAGACCGACGACCGGAATAATGACCCCCCACACGGTAATGCTACTGATTTGCCCGGTAATgcg  >  1:992940/1‑68 (MQ=255)

                                                       atGCACAGACCGACGACCGGAATAATGACCCCCCACACGGTAATGCTACTGATTTGCCCGGTAATgcg  >  1:792781/1‑68 (MQ=255)

                                                       atGCACAGACCGACGACCGGAATAATGACCCCCCACACGGTAATGCTACTGATTTGCCCGGTAATgcg  >  1:959992/1‑68 (MQ=255)

                                                       atGCACAGACCGACGACCGGAATAATGACCCCCCACACGGTAATGCTACTGATTTGCCCGGTAATgcg  >  1:3331839/1‑68 (MQ=255)

                                                       atGCACAGACCGACGACCGGAATAATGACCCCCCACACGGTAATGCTACTGATTTGCCCGGTAATgcg  >  1:3293069/1‑68 (MQ=255)

                                                       atGCACAGACCGACGACCGGAATAATGACCCCCCACACGGTAATGCTACTGATTTGCCCGGTAATgcg  >  1:2973051/1‑68 (MQ=255)

                                                       atGCACAGACCGACGACCGGAATAATGACCCCCCACACGGTAATGCTACTGATTTGCCCGGTAATgcg  >  1:2623765/1‑68 (MQ=255)

                                                       atGCACAGACCGACGACCGGAATAATGACCCCCCACACGGTAATGCTACTGATTTGCCCGGTAATgcg  >  1:123235/1‑68 (MQ=255)

                                                       atGCACAGACCGACGACCGGAATAATGACCCCCCACACGGTAATGCTACTGATTTGCCCGGTAATgcg  >  1:1057348/1‑68 (MQ=255)

ATGCGGATTCCAGGAATCAACGTACAGCGTCGGGCTAAACCAGAACCAGCCAATAATGCACAGACCGACGACCGGAATAATGACCCCCCACACGGTAATGCTACTGATTTGCCCGGTAATGCG  >  minE/441015‑441137

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