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
A5 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,771,105 G→A 40.5% N79N (AAC→AAT)  ypjL ← predicted inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,771,1050GA40.5% 53.2 / 86.0 74N79N (AAC→AAT) ypjLpredicted inner membrane protein
Reads supporting (aligned to +/- strand):  ref base G (21/23);  new base A (14/16);  total (35/39)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01

CCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGCCCATAACCCCTTGTC  >  W3110S.gb/2771035‑2771173
                                                                      |                                                                    
ccTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTg                                                                      <  1:2090699/71‑1 (MQ=255)
 ctctTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGt                                                                     <  1:3002205/71‑1 (MQ=255)
      tGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTtc                                                                   <  1:2497875/68‑1 (MQ=255)
      tGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTtc                                                                   <  1:1628547/68‑1 (MQ=255)
         cgacgCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTATTCATCACt                                                             <  1:399211/71‑1 (MQ=255)
             gCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACtgat                                                          >  1:438848/1‑70 (MQ=255)
             gCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACtgat                                                          >  1:4166184/1‑70 (MQ=255)
              ccAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTATtcat                                                                 <  1:2217661/62‑1 (MQ=255)
              ccAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTATTCATCACtgatga                                                        <  1:3464561/71‑1 (MQ=255)
                aGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTATTCATCACt                                                             <  1:1579971/64‑1 (MQ=255)
                  tCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTATtcat                                                                 <  1:1228548/58‑1 (MQ=255)
                   cGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTATTCATCACTGATgagaga                                                    >  1:3497944/1‑70 (MQ=255)
                   cGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTATTCATCACTGATgagaga                                                    >  1:3497942/1‑70 (MQ=255)
                    gCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTATTCATCACTGATGAGAGaaa                                                  >  1:253564/1‑71 (MQ=255)
                    gCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTATTCATCACTGATGAGAGaaa                                                  >  1:3701873/1‑71 (MQ=255)
                     ccGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAAt                                                 >  1:4373814/1‑71 (MQ=255)
                       gTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTATTCATCACTGATGAGAGAAATGc                                               <  1:522743/71‑1 (MQ=255)
                          cTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGt                                            >  1:2772654/1‑71 (MQ=255)
                          cTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTATTCATCACt                                                             <  1:4061904/54‑1 (MQ=255)
                          cTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTATTCATCACt                                                             <  1:2377719/54‑1 (MQ=255)
                          cTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTATTCATCACt                                                             <  1:119961/54‑1 (MQ=255)
                          cTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTATTCATCACt                                                             <  1:4879429/54‑1 (MQ=255)
                          cTCCCGTCAATCGACAGCGCA‑CAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTc                                           <  1:2640012/71‑1 (MQ=255)
                            cccGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTATTCATCACTGATGAGAGaa                                                   >  1:3929727/1‑62 (MQ=255)
                             ccGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCa                                          <  1:3668276/70‑1 (MQ=255)
                             ccGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCa                                          <  1:5089026/70‑1 (MQ=255)
                              cGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCaag                                        <  1:24196/71‑1 (MQ=255)
                              cGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCaag                                        <  1:274658/71‑1 (MQ=255)
                                 cAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACtgatga                                                        >  1:4455891/1‑52 (MQ=255)
                                 cAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACtgatga                                                        >  1:3433357/1‑52 (MQ=255)
                                 cAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACtgatga                                                        >  1:866418/1‑52 (MQ=255)
                                 cAATCGACAGCGCACCAATCAGCACCGTCGGCATATTATTCATCACTGATGAGAGAAATGCCGTCaagaag                                     >  1:3824161/1‑71 (MQ=255)
                                    tCGACAGCGCACCAATCAGCACCGTCGGCATATTGtt                                                                    <  1:3716232/37‑1 (MQ=255)
                                    tCGACAGCGCACCAATCAGCACCGTCGGCATATTGtt                                                                    <  1:2938009/37‑1 (MQ=255)
                                          gcgcACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCg                            <  1:1417825/71‑1 (MQ=255)
                                           cgcACCAATCAGCACCGTCGGCATATTATTCATCACTGATgaga                                                      >  1:2846968/1‑44 (MQ=255)
                                              aCCAATCAGCACCGTCGGCATATTGTTCATCACTGATgagaga                                                    <  1:1344186/43‑1 (MQ=255)
                                                cAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGCACGTc                      >  1:245458/1‑71 (MQ=255)
                                                 aaTCAGCACCGTCGGCATATTGTTCATCACTGATgagaga                                                    >  1:3163352/1‑40 (MQ=255)
                                                  aTCAGCACCGTCGGCATATTGTTCATCACTGATgagaga                                                    >  1:1222380/1‑39 (MQ=255)
                                                  aTCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGc                    >  1:4194042/1‑71 (MQ=255)
                                                   tCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGc                                    <  1:3368452/54‑1 (MQ=255)
                                                   tCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGc                                    <  1:1409992/54‑1 (MQ=255)
                                                   tCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCt                   >  1:2929147/1‑71 (MQ=255)
                                                    cAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTg                  >  1:3577284/1‑71 (MQ=255)
                                                     aGCACCGTCGGCATATTGTTCATCACTGATGAGAGaaa                                                  >  1:3356088/1‑38 (MQ=255)
                                                     aGCACCGTCGGCATATTATTCATCACTGATGAGAGaaa                                                  >  1:3314914/1‑38 (MQ=255)
                                                     aGCACCGTCGGCATATTATTCATCACTGATGAGAGaaa                                                  >  1:732278/1‑38 (MQ=255)
                                                     aGCACCGTCGGCATATTATTCATCACTGATGAGAGaaa                                                  >  1:1405469/1‑38 (MQ=255)
                                                     aGCACCGTCGGCATATTATTCATCACTGATGAGAGAAATGCCGTCaagaa                                      >  1:3981796/1‑50 (MQ=255)
                                                      gCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGcc                >  1:3154163/1‑71 (MQ=255)
                                                      gCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGc                 >  1:2595373/1‑70 (MQ=255)
                                                       cACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGccc               <  1:4799117/71‑1 (MQ=255)
                                                        aCCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGccc               <  1:2033494/70‑1 (MQ=255)
                                                        aCCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGccc               <  1:2462938/70‑1 (MQ=255)
                                                         ccGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGCCCa              >  1:4573591/1‑70 (MQ=255)
                                                          cGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGc                 <  1:3166498/66‑1 (MQ=255)
                                                            tCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTc                      <  1:3537837/59‑1 (MQ=255)
                                                            tCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTc                      <  1:3543949/59‑1 (MQ=255)
                                                            tCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTc                      <  1:696045/59‑1 (MQ=255)
                                                            tCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTg                  >  1:1139578/1‑63 (MQ=255)
                                                            tCGGCATATTATTCATCACTGATGAGAGAAATGCCTTCAAGAAGCCGGTGCCGAACGTCGCTGCCCATAAc          <  1:1052405/71‑1 (MQ=255)
                                                            tCGGCATATTATTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGCCCATAAc          <  1:1999646/71‑1 (MQ=255)
                                                            tCGGCATATTATTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGCCCATAAc          >  1:1028586/1‑71 (MQ=255)
                                                              ggCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGCCCATAAccc        >  1:3850929/1‑71 (MQ=255)
                                                               gCATATTATTCATCACTGATGAGAGAAATGCCGTCa                                          <  1:2626484/36‑1 (MQ=255)
                                                               gCATATTATTCATCACTGATGAGAGAAATGCCGTCa                                          <  1:4795969/36‑1 (MQ=255)
                                                               gCATATTATTCATCACTGATGAGAGAAATGCCGTCa                                          <  1:2388668/36‑1 (MQ=255)
                                                               gCATATTATTCATCACTGATGAGAGAAATGCCGTCa                                          <  1:3207913/36‑1 (MQ=255)
                                                                 atatTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGCCCATAACCCCtt     <  1:1498211/71‑1 (MQ=255)
                                                                 atatTATTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCgg                                 >  1:1095447/1‑43 (MQ=255)
                                                                 atatTATTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGCCCATAACCCCtt     >  1:243528/1‑71 (MQ=255)
                                                                    ttGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGCCCAt             <  1:272183/60‑1 (MQ=255)
                                                                    ttGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGCCCATAACCCCTTGTc  >  1:1295631/1‑71 (MQ=255)
                                                                    ttGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGCCCATAACCCCTTGTc  >  1:1301549/1‑71 (MQ=255)
                                                                      |                                                                    
CCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGAAATGCCGTCAAGAAGCCGGTGCCGAACGTCGCTGCCCATAACCCCTTGTC  >  W3110S.gb/2771035‑2771173

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