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 F3 I0 R2 232 76.3 4135488 90.9% 3759158 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,845,199 G→T 58.3% P266T (CCG→ACG)  cysD ← sulfate adenylyltransferase, subunit 2

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,845,1990GT58.3% ‑4.9 / 88.6 60P266T (CCG→ACG) cysDsulfate adenylyltransferase, subunit 2
Reads supporting (aligned to +/- strand):  ref base G (11/14);  new base T (27/8);  total (38/22)
Fisher's exact test for biased strand distribution p-value = 1.40e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGTCGCGGTCAATCACGCGGCCCTGACGTTCACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGGCAGTGTTTGTGCATTTGACTCCACCGCACCGGTCAGCGGCCAGCAGCCCAGCGTACGGAAACGCAC  >  minE/1845130‑1845265
                                                                     |                                                                  
ggTCGCGGTCAATCACGCGGCCCTGACGTTCACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCgg                                                                    >  1:2326003/1‑70 (MQ=255)
      ggTCAATCACGCGGCCCTGACGTTCACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGGCAGTGtt                                                             <  1:1868542/71‑1 (MQ=255)
             cACGCGGCCCTGACGTTCACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGGCAGTGTTTGTGCAt                                                      >  1:2231732/1‑71 (MQ=255)
             cACGCGGCCCTGACGTTCACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGGCAGTGTTTGTGCAt                                                      >  1:123703/1‑71 (MQ=255)
               cgcgGCCCTGACGTTCACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGTCAGTGTTTGTGCAttt                                                    <  1:2665208/71‑1 (MQ=255)
                     ccTGACGTTCACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGTCAGTGTTTGTGCATTTGACTcc                                              <  1:4078601/71‑1 (MQ=255)
                      cTGACGTTCACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGTCAGTGTTTGTGCa                                                       <  1:3122526/61‑1 (MQ=255)
                         aCGTTCACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGTCAGTGTTTGTGCATTTGACTCcaccg                                          >  1:3982396/1‑71 (MQ=255)
                         aCGTTCACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGTCAGTGTTTGTGCATTTGACTCcaccg                                          >  1:2432705/1‑71 (MQ=255)
                         aCGTTCACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGTCAGTGTTTGTGCATTTGACTCcaccg                                          >  1:3716515/1‑71 (MQ=255)
                         aCGTTCACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGTCAGTGTTTGTGCATTTGACTCcacc                                           >  1:3810801/1‑70 (MQ=255)
                            ttCACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGGCAGTGTTTGTGCa                                                       <  1:225700/55‑1 (MQ=255)
                            ttCACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGGCAGTGTTTGTGCATTTGAc                                                 <  1:3381016/61‑1 (MQ=255)
                            ttCACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGGCAGTGTTTGTGCATTTGAc                                                 <  1:3621863/61‑1 (MQ=255)
                            ttCACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGGCAGTGTTTGTGCATTTGAc                                                 <  1:952708/61‑1 (MQ=255)
                            ttCACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGGCAGTGTTTGTGCATTTGAc                                                 <  1:1366605/61‑1 (MQ=255)
                            ttCACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGGCAGTGTTTGTGCATTTGAc                                                 <  1:3254711/61‑1 (MQ=255)
                              cACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGTCAGTGttt                                                            >  1:2258194/1‑48 (MQ=255)
                              cACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGTCAGTGttt                                                            >  1:4085524/1‑48 (MQ=255)
                              cACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGTCAGTGttt                                                            >  1:3728738/1‑48 (MQ=255)
                              cACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGTCAGTGttt                                                            >  1:3172669/1‑48 (MQ=255)
                              cACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGTCAGTGttt                                                            >  1:1128256/1‑48 (MQ=255)
                              cACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGTCAGTGTTTGTGCAttt                                                    >  1:2161387/1‑56 (MQ=255)
                              cACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGTCAGTGTTTGTGCAttt                                                    >  1:491418/1‑56 (MQ=255)
                              cACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGTCAGTGTTTGTGCAttt                                                    >  1:3005487/1‑56 (MQ=255)
                              cACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGTCAGTGTTTGTGCAttt                                                    >  1:2861003/1‑56 (MQ=255)
                                  ggtggtggAAACCAGCATCTCTTCGATGATTTCCGGCAGTGttt                                                            >  1:2450041/1‑44 (MQ=255)
                                   gtggtggAAACCAGCATCTCTTCGATGATTTCCGTCAGTGTTtg                                                           >  1:2462366/1‑44 (MQ=255)
                                   gtggtggAAACCAGCATCTCTTCGATGATTTCCGTCAGTGTTtg                                                           >  1:2633718/1‑44 (MQ=255)
                                   gtggtggAAACCAGCATCTCTTCGATGATTTCCGTCAGTGTTtg                                                           >  1:2467105/1‑44 (MQ=255)
                                   gtggtggAAACCAGCATCTCTTCGATGATTTCCGTCAGTGTTtg                                                           >  1:1009203/1‑44 (MQ=255)
                                        ggAAACCAGCATCTCTTCGATGATTTCCGTCAGTGTTTGTGCATTTGACTCCACCGCACCGGTCAGCGGc                            >  1:2622459/1‑70 (MQ=255)
                                           aaCGAGCATCTCTTCGATGATTTCCGTCAGTGTTTGTGCATTTGACTCcac                                            >  1:2058053/1‑51 (MQ=38)
                                           aaCCAGCATCTCTTCGATGATTTCCGTCAGTGTTTGTGCATTTGACTCcac                                            >  1:2708077/1‑51 (MQ=255)
                                           aaCCAGCATCTCTTCGATGATTTCCGTCAGTGTTTGTGCATTTGACTCcac                                            >  1:2653799/1‑51 (MQ=255)
                                           aaCCAGCATCTCTTCGATGATTTCCGTCAGTGTTTGTGCATTTGACTCcac                                            >  1:3909150/1‑51 (MQ=255)
                                           aaCCAGCATCTCTTCGATGATTTCCGTCAGTGTTTGTGCATTTGACTCcac                                            >  1:720476/1‑51 (MQ=255)
                                           aaCCAGCATCTCTTCGATGATTTCCGTCAGTGTTTGTGCATTTGACTCcac                                            >  1:1208080/1‑51 (MQ=255)
                                           aaCCAGCATCTCTTCGATGATTTCCGTCAGTGTTTGTGCATTTGACTCcac                                            >  1:1065515/1‑51 (MQ=255)
                                           aaCCAGCATCTCTTCGATGATTTCCGTCAGTGTTTGTGCATTTGACTCca                                             >  1:29005/1‑50 (MQ=255)
                                               aGCATCTCTTCGATGATTTCCGGCAGTGTTTGTGCATTTGACTCcac                                            >  1:354046/1‑47 (MQ=255)
                                               aGCATCTCTTCGATGATTTCCGGCAGTGTTTGTGCATTTGACTCcac                                            >  1:583490/1‑47 (MQ=255)
                                               aGCATCTCTTCGATGATTTCCGGCAGTGTTTGTGCATTTGACTCcac                                            >  1:2771718/1‑47 (MQ=255)
                                               aGCATCTCTTCGATGATTTCCGGCAGTGTTTGTGCATTTGACTCca                                             >  1:1103106/1‑46 (MQ=255)
                                                         cGATGATTTCCGGCAGTGTTTGTGCATTTGACTCCACCGCACCGGTCTGCGGCCAGCAGCCCAGCGTACg           <  1:2877958/70‑1 (MQ=255)
                                                         cGATGATTTCCGGCAGTGTTTGTGCATTTGACTCCACCGCACCGGTCAGCGGCCAGCAGCCCAGCGTACg           <  1:95397/70‑1 (MQ=255)
                                                         cGATGATTTCCGGCAGTGTTTGTGCATTTGACTCCACCGCACCGGTCAGCGGCCAGCAGCCCAGCGTACg           >  1:813603/1‑70 (MQ=255)
                                                         cGATGATTTCCGGCAGTGTTTGTGCATTTGACTCCACCGCACCGGTCAGCGGCCAGCAGCCCAGCGTACg           <  1:1213778/70‑1 (MQ=255)
                                                         cGATGATTTCCGGCAGTGTTTGTGCATTTGACTCCACCGCACCGGTCAGCGGCCAGCAGCCCAGCGTACg           >  1:2130439/1‑70 (MQ=255)
                                                         cGATGATTTCCGGCAGTGTTTGTGCATTTGACTCCACCGCACCGGTCAGCGGCCAGCAGCCCAGCGTACg           <  1:4084179/70‑1 (MQ=255)
                                                             gatTTCCGGCAGTGTTTGTGCATTTGACTCCACCGCACCGGTCAGCGGCCAGCAGCCCAGCGTACGGAAAc      >  1:3580250/1‑71 (MQ=255)
                                                              atTTCCGTCAGTGTTTGTGCATTTGACTCCACCGCACCGGTCAGCGGCCAGCAGCCCAGCGTACGGAAACg     <  1:4001539/71‑1 (MQ=255)
                                                              atTTCCGTCAGTGTTTGTGCATTTGACTCCACCGCACCGGTCAGCGGCCAGCAGCCCAGCGTACGGAAACg     <  1:4128023/71‑1 (MQ=255)
                                                              atTTCCGTCAGTGTTTGTGCATTTGACTCCACCGCACCGGTCAGCGGCCAGCAGCCCAGCGTACGGAAACg     <  1:2098241/71‑1 (MQ=255)
                                                              atTTCCGTCAGTGTTTGTGCATTTGACTCCACCGCACCGGTCAGCGGCCAGCAGCCCAGCGTACGGAAACg     <  1:3236112/71‑1 (MQ=255)
                                                              atTTCCGTCAGTGTTTGTGCATTTGACTCCACCGCACCGGTCAGCGGCCAGCAGCCCAGCGTACGGAAACg     <  1:929744/71‑1 (MQ=255)
                                                              atTTCCGGCAGTGTTTGTGCATTTGACTCCACCGCACCGGTCAGCGGCCAGCAGCCCAGCGTACGGAAACg     <  1:3175595/71‑1 (MQ=255)
                                                               tttCCGGCAGTGTTTGTGCATTTGACTCCACCGCACCGGTCAGCGGCCAGCAGCCCAGCGTACGGAAACg     <  1:3725251/70‑1 (MQ=255)
                                                                ttCCGTCAGTGTTTGTGCATTTGACTCCACCGCACCGGTCAGCGGCCAGCAGCCCAGCGTACGGAAACg     >  1:636167/1‑69 (MQ=255)
                                                                ttCCGGCAGTGTTTGTGCATTTGACTCCACCGCACCGGTCAGCGGCCAGCAGCCCAGCGTACg           <  1:1032661/63‑1 (MQ=255)
                                                                 tCCGGCAGTGTTTGTGCATTTGACTCCACCGCACCGGTCAGCGGCCAGCAGCCCAGCGTACGGAAACGCAc  >  1:957526/1‑71 (MQ=255)
                                                                     |                                                                  
GGTCGCGGTCAATCACGCGGCCCTGACGTTCACTGGTGGTGGAAACCAGCATCTCTTCGATGATTTCCGGCAGTGTTTGTGCATTTGACTCCACCGCACCGGTCAGCGGCCAGCAGCCCAGCGTACGGAAACGCAC  >  minE/1845130‑1845265

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A