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	691,194	G→A	61.8%	A414A (GCG→GCA)	hyaB →	hydrogenase 1, large subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	691,194	0	G	A	61.8%	31.4 / 43.6	68	A414A (GCG→GCA)	hyaB	hydrogenase 1, large subunit
Reads supporting (aligned to +/- strand): ref base G (10/16); new base A (27/15); total (37/31)
Fisher's exact test for biased strand distribution p-value = 4.75e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.33e-01

AACGCTACTCGTGGATCAAAGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCGCGCACGTTAATCGCTTATCACAAAGGCGATGCTGCGACCG  >  minE/691130‑691234

aaCGCTACTCGTGGATCAAAGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCGCGCa                                      <  1:1073374/69‑1 (MQ=255)

aaCGCTACTCGTGGATCAAAGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCGCGCa                                      <  1:962670/69‑1 (MQ=255)

aaCGCTACTCGTGGATCAAAGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCGCGCa                                      <  1:380600/69‑1 (MQ=255)

aaCGCTACTCGTGGATCAAAGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCGCGCa                                      <  1:3380584/69‑1 (MQ=255)

aaCGCTACTCGTGGATCAAAGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCGCGCa                                      <  1:1194113/69‑1 (MQ=255)

         cGTGGATCAAAGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCGCGCACGTTAATCg                             >  1:1253172/1‑69 (MQ=255)

             gATCAAAGCGCCACTCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCGCGCACGTTAATCGCtt                          >  1:2959990/1‑68 (MQ=255)

             gATCAAAGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCGCGCACGTTAATCGCtt                          >  1:1911220/1‑68 (MQ=255)

             gATCAAAGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCGCGCACGTTAATCGCtt                          >  1:2678882/1‑68 (MQ=255)

             gATCAAAGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCGCGCACGTTAATCGCtt                          >  1:1380482/1‑68 (MQ=255)

             gATCAAAGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCGCGCACGTTAATCGCtt                          >  1:3245645/1‑68 (MQ=255)

             gATCAAAGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCGCGCACGTTAATCGCtt                          >  1:23869/1‑68 (MQ=255)

             gATCAAAGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCGCGCACGTTAATCGCtt                          >  1:705851/1‑68 (MQ=255)

             gATCAAAGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCGCGCACGTTAATCGCtt                          >  1:2500614/1‑68 (MQ=255)

             gATCAAAGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCGCGCACGTTAATCGCtt                          >  1:1529586/1‑68 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATc                              >  1:2803746/1‑59 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:2520197/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:2462620/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:3216975/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:3038861/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:2293259/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:2554443/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:2048544/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:2174973/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:2154910/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:2133456/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:3259025/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:3314666/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:1752561/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:1246531/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:80295/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:14010/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:1432075/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:1456936/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:766517/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:1492736/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:1680826/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:596536/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:566643/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:2003871/1‑67 (MQ=255)

                  aaGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:1118254/1‑67 (MQ=255)

                  aaGCGCAACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATca                      >  1:437319/1‑67 (MQ=255)

                     cgcCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCC‑CTGGCACGCACGTTAATCGCTTATCACAAAgg                <  1:1991758/69‑1 (MQ=255)

                      gcCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATCACAAAgg                <  1:3319972/69‑1 (MQ=255)

                      gcCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATCACAAAgg                <  1:422045/69‑1 (MQ=255)

                      gcCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATCACAAAgg                <  1:2994613/69‑1 (MQ=255)

                      gcCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATCACAAAgg                <  1:2392063/69‑1 (MQ=255)

                      gcCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATCACAAAgg                <  1:2543818/69‑1 (MQ=255)

                      gcCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATCACAAAgg                <  1:2197968/69‑1 (MQ=255)

                      gcCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATCACAAAgg                <  1:2079245/69‑1 (MQ=255)

                      gcCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATCACAAAgg                <  1:1329643/69‑1 (MQ=255)

                      gcCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATCACAAAgg                <  1:147897/69‑1 (MQ=255)

                      gcCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATCACAAAgg                <  1:2844974/69‑1 (MQ=255)

                      gcCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATCACAAAgg                <  1:1897438/69‑1 (MQ=255)

                      gcCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATCACAAAgg                <  1:1844263/69‑1 (MQ=255)

                       ccACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATCACAAAgg                <  1:757717/68‑1 (MQ=255)

                                  cgGTAACGCGATGGAAGTGGGGCCGCTGGCGCGCACGTTAATCGCTTATCACAAAGGCGATGCTGCGAc    <  1:2521758/69‑1 (MQ=255)

                                  cgGTAACGCGATGGAAGTGGGGCCGCTGGCGCGCACGTTAATCGCTTATCACAAAGGCGATGCTGCGAc    <  1:572950/69‑1 (MQ=255)

                                    gTAACGCGATGGATGTGGGGCCGCTGGCGCGCACGTTAATCGCTTATCACAAAGGCGATGCTGCGACCg  <  1:2602077/69‑1 (MQ=255)

                                    gTAACGCGATGGAAGTGGGGCCGCTGGCACGCACGTTAATCGCTTATCACAAAgg                <  1:205204/55‑1 (MQ=255)

                                      aaCGCGATGGAAGTGGGGCCGCTGGCGCGCACGTTAATCGCTTATCACAAAGGCGAt            <  1:1091972/57‑1 (MQ=255)

                                      aaCGCGATGGAAGTGGGGCCGCTGGCGCGCACGTTAATCGCTTATCACAAAGGCGAt            <  1:1051755/57‑1 (MQ=255)

                                      aaCGCGATGGAAGTGGGGCCGCTGGCGCGCACGTTAATCGCTTATCACAAAGGCGAt            <  1:149107/57‑1 (MQ=255)

                                      aaCGCGATGGAAGTGGGGCCGCTGGCGCGCACGTTAATCGCTTATCACAAAGGCGAt            <  1:1820291/57‑1 (MQ=255)

                                      aaCGCGATGGAAGTGGGGCCGCTGGCGCGCACGTTAATCGCTTATCACAAAGGCGAt            <  1:1865591/57‑1 (MQ=255)

                                      aaCGCGATGGAAGTGGGGCCGCTGGCGCGCACGTTAATCGCTTATCACAAAGGCGAt            <  1:2065336/57‑1 (MQ=255)

                                      aaCGCGATGGAAGTGGGGCCGCTGGCGCGCACGTTAATCGCTTATCACAAAGGCGAt            <  1:2075979/57‑1 (MQ=255)

                                                            tGGCGCGCACGTTAATCGCTTATCACAAAGGCGATGCTGCGAc    <  1:2623436/43‑1 (MQ=255)

AACGCTACTCGTGGATCAAAGCGCCACGCTGGCGCGGTAACGCGATGGAAGTGGGGCCGCTGGCGCGCACGTTAATCGCTTATCACAAAGGCGATGCTGCGACCG  >  minE/691130‑691234

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